What changed in this filing

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Item 9A. Controls and Procedures

2024-02-21 compared with 2023-02-17 · 469 added, 514 removed, 972 unchanged (50% of the section changed)

1 unchanged sentence

Evaluation of Disclosure Controls and Procedures

Management carried out an evaluation, under the supervision and with the participation of our Principal Executive Officer and Principal Financial Officer, of the effectiveness of our “disclosure controls and procedures”

as of the end of the period covered by this Annual Report, pursuant to Rules 13a-15(e) and 15d-15(e) under the Securities Exchange Act of 1934, or the Exchange Act.

Based on this evaluation, our Principal Executive Officer and Principal Financial Officer concluded that our disclosure controls and procedures were effective and designed to provide reasonable assurance that the information required to be disclosed is recorded, processed, summarized, and reported within the time periods specified in the SEC rules and forms as of December 31, 2022.

For the purpose of this review, disclosure controls and procedures means controls and procedures designed to ensure that information required to be disclosed by us in the reports that we file or submit is recorded, processed, summarized and reported within the time periods specified in the SEC’s rules and forms.

These disclosure controls and procedures include, without limitation, controls and procedures designed to ensure that information required to be disclosed by us in the reports that we file or submit is accumulated and communicated to management, including our Principal Executive Officer and Principal Financial Officer, as appropriate to allow timely decisions regarding required disclosure.

Management carried out an evaluation, under the supervision and with the participation of our Principal Executive Officer and our Principal Financial Officer, of the effectiveness of our “disclosure controls and procedures” as of the end of the period covered by this Annual Report, pursuant to Rules 13a-15(e) and 15d-15(e) under the Securities Exchange Act of 1934, or the Exchange Act.

In connection with that evaluation, our Principal Executive Officer and our Principal Financial Officer concluded that our disclosure controls and procedures were effective and designed to provide reasonable assurance that the information required to be disclosed is recorded, processed, summarized, and reported within the time periods specified in the SEC rules and forms as of December 31, 2023.

These disclosure controls and procedures include, without limitation, controls and procedures designed to ensure that information required to be disclosed by us in the reports that we file or submit is accumulated and communicated to management, including our Principal Executive Officer and our Principal Financial Officer, as appropriate to allow timely decisions regarding required disclosure.

In designing and evaluating the disclosure controls and procedures, our management recognizes that any controls and procedures, no matter how well designed and operated, can provide only reasonable assurance of achieving the desired control objectives, and our management necessarily applies its judgment in evaluating the cost-benefit relationship of possible controls and procedures.

Management’s Annual Report on Internal Control Over Financial Reporting

Management is responsible for establishing and maintaining adequate internal control over financial reporting as defined in Rules 13a-15(f) and 15d-15(f) of the Exchange Act.

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Opinion on Internal Control Over Financial Reporting

We have audited Ultragenyx Pharmaceutical Inc.’s internal control over financial reporting as of December 31, 2022, based on criteria established in Internal Control—Integrated Framework issued by the Committee of Sponsoring Organizations of the Treadway Commission ( 2013 framework) (the COSO criteria).

We have audited Ultragenyx Pharmaceutical Inc.’s internal control over financial reporting as of December 31, 2023, based on criteria established in Internal Control—Integrated Framework issued by the Committee of Sponsoring Organizations of the

Treadway Commission ( 2013 framework) (the COSO criteria).

In our opinion, Ultragenyx Pharmaceutical Inc.

(the Company) maintained, in all material respects, effective internal control over financial reporting as of December 31, 2023, based on the COSO criteria.

We also have audited, in accordance with the standards of the Public Company Accounting Oversight Board (United States) (PCAOB), the consolidated balance sheets of Ultragenyx Pharmaceutical Inc.

as of December 31, 2022 and 2021, the related consolidated statements of operations, comprehensive loss, stockholders’

equity and cash flows for each of the three years in the period ended December 31, 2022, and the related notes, and our report dated February 16, 2023 expressed an unqualified opinion thereon.

We also have audited, in accordance with the standards of the Public Company Accounting Oversight Board (United States) (PCAOB), the consolidated balance sheets of the Company as of December 31, 2023 and 2022, the related consolidated statements of operations, comprehensive loss, stockholders’ equity and cash flows for each of the three years in the period ended December 31, 2023, and the related notes and our report dated February 21, 2024 expressed an unqualified opinion thereon.

Basis for Opinion

The Company’s management is responsible for maintaining effective internal control over financial reporting and for its assessment of the effectiveness of internal control over financial reporting included in the accompanying Management’s Annual Report on Internal Control over Financial Reporting.

Our responsibility is to express an opinion on the Company’s internal control over financial reporting based on our audit.

We are a public accounting firm registered with the PCAOB and are required to be independent with respect to the Company in accordance with the U.S.

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Definition and Limitations of Internal Control Over Financial Reporting

A company’s internal control over financial reporting is a process designed to provide reasonable assurance regarding the reliability of financial reporting and the preparation of financial statements for external purposes in accordance with generally accepted accounting principles.

A company’s internal control over financial reporting includes those policies and procedures that (1) pertain to the maintenance of records that, in reasonable detail, accurately and fairly reflect the transactions and dispositions of the assets of the company;

(2) provide reasonable assurance that transactions are recorded as necessary to permit preparation of financial statements in accordance with generally accepted accounting principles, and that receipts and expenditures of the company are being made only in accordance with authorizations of management and directors of the company;

and (3) provide reasonable assurance regarding prevention or timely detection of unauthorized acquisition, use, or disposition of the company’s assets that could have a material effect on the financial statements.

Because of its inherent limitations, internal control over financial reporting may not prevent or detect misstatements.

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Other Information

On November 10, 2023 , Corsee Sanders , Ph.D., a member of the Company’s Board of Directors , adopted a trading arrangement intended to satisfy the affirmative defense of Rule 10b5-1(c), to sell up to 2,322 shares of the Company’s common stock through July 12, 2024, subject to certain conditions.

On December 7, 2023 , Matthew Fust , a member of the Company’s Board of Directors , adopted a trading arrangement intended to satisfy the affirmative defense of Rule 10b5-1(c), to sell up to 12,195 shares of the Company’s common stock through December 6, 2024, subject to certain conditions.

Disclosure Regarding Foreign Jurisdictions that Prevent Inspections

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Di rectors, Executive Officers and Corporate Governance

Except as set forth below, the information required by this Item is incorporated herein by reference to information in the proxy statement for our 2023 Annual Meeting of Stockholders, which we will file with the SEC within 120 days of the end of the fiscal year to which this Annual Report relates, or the “2023 Proxy Statement”, including under the headings “Nominees and Incumbent Directors,”

“Executive Officers,”

““Board of Directors and Committees,”

and, as applicable, “Delinquent Section 16(a) Beneficial Ownership Reports.”

We have adopted a code of ethics that applies to all of our directors, officers and employees, including our principal executive, principal financial and principal accounting officers, or persons performing similar functions, or Code of Ethics.

Our Code of Ethics is posted on our website located at https://ir.ultragenyx.com/ under “Corporate Governance”.

Except as set forth below, the information required by this Item is incorporated herein by reference to information in the proxy statement for our 2024 Annual Meeting of Stockholders, which we will file with the SEC within 120 days of the end of the fiscal year to which this Annual Report relates, or the “2024 Proxy Statement”, including under the headings “Nominees and Incumbent Directors,” “Executive Officers,” ““Board of Directors and Committees,” and, as applicable, “Delinquent Section 16(a) Beneficial Ownership Reports.” We have adopted a code of ethics that applies to all of our directors, officers and employees, including our principal executive, principal financial and principal accounting officers, or persons performing similar functions, or Code of Ethics.

Our Code of Ethics is posted on our website located at https://ir.ultragenyx.com/ under “Corporate Governance”.

We intend to disclose future amendments to certain provisions of the Code of Ethics, and waivers of the Code of Ethics granted to executive officers and directors, on the website within four business days following the date of the amendment or waiver.

Executive Compensation

The information required by this Item is incorporated herein by reference to information in the 2023 Proxy Statement, including under the headings “Executive Compensation,”

“Director Compensation,”

and “Board of Directors and Committees”

The information required by this Item is incorporated herein by reference to information in the 2024 Proxy Statement, including under the headings “Executive Compensation,” “Director Compensation,” and “Board of Directors and Committees.”

Security Ownership of Certain Beneficial Owners and Management and Related Stockholder Matters

The information required by this Item is incorporated herein by reference to information in the 2023 Proxy Statement, including under the headings “Security Ownership of Certain Beneficial Owners and Management”

and “Equity Compensation Plan Information.”

The information required by this Item is incorporated herein by reference to information in the 2024 Proxy Statement, including under the headings “Security Ownership of Certain Beneficial Owners and Management” and “Equity Compensation Plan Information.”

Certain Relationships and Related Transactions, and Director Independence

The information required by this Item is incorporated herein by reference to information in the 2023 Proxy Statement, including under the headings “Certain Relationships and Related-Person Transactions,”

“Corporate Governance,”

and “Board of Directors and Committees.”

The information required by this Item is incorporated herein by reference to information in the 2024 Proxy Statement, including under the headings “Certain Relationships and Related-Person Transactions,” “Corporate Governance,” and “Board of Directors and Committees.”

Principal Accountant Fees and Services

The information required by this Item is incorporated herein by reference to information in the 2023 Proxy Statement, including under the heading “Proposal No.

2—Ratification of the Selection of Independent Registered Public Accounting Firm.”

The information required by this Item is incorporated herein by reference to information in the 2024 Proxy Statement, including under the heading “Proposal No.

3—Ratification of the Selection of Independent Registered Public Accounting Firm.”

Ex hibits and Financial Statement Schedules

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(1) Consolidated Financial Statements

Consolidated Financial Statements—See Index to Consolidated Financial Statements at page F-1 of this Annual Report.

(2) Consolidated Financial Statement Schedules

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Amended and Restated Certificate of Incorporation

Amended and Restated Bylaws

Second Amended and Restated Bylaws

Form of Common Stock Certificate

Form of Indenture

Form of Pre-Funded Warrant

Description of Common Stock

Open Market Sales Agreement, dated May 7, 2021, between Ultragenyx Pharmaceutical Inc.

and Jefferies LLC

Collaboration and License Agreement, effective as of August 29, 2013, between Ultragenyx Pharmaceutical Inc.

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and Kyowa Kirin Co., Ltd.

License Agreement, dated as of September 20, 2012, between Ultragenyx Pharmaceutical Inc.

and Baylor Research Institute

Amendment to the License Agreement, dated as of March 22, 2013, between Ultragenyx Pharmaceutical Inc.

and Baylor Research Institute

Exclusive License Agreement, dated as of November 22, 2010, between Ultragenyx Pharmaceutical Inc.

and Saint Louis University

License Agreement, dated October 30, 2013, between Dimension Therapeutics, Inc.

and REGENXBIO Inc.

(f/k/a ReGenX Biosciences, LLC), as amended

Option and License Agreement, dated March 10, 2015, between Dimension Therapeutics, Inc.

and REGENXBIO Inc.

First Amendment to Option and License Agreement, dated March 18, 2019, between REGENXBIO, Inc.

and Ultragenyx Pharmaceutical Inc.

(as assignee of Dimension Therapeutics, Inc.)

Second Amendment to Option and License Agreement, dated December 17, 2021, between REGENXBIO, Inc.

and Ultragenyx Pharmaceutical Inc.

Research, Collaboration and License Agreement, dated as of May 5, 2016, between Dimension Therapeutics, Inc.

and The Trustees of the University of Pennsylvania, as amended

3rd Amendment to Research, Collaboration and License Agreement, entered into as of October 30, 2017, between Dimension Therapeutics, Inc.

and The Trustees of the University of Pennsylvania

Commercial Supply and Services Agreement –

Drug Substance, effective December 7, 2017, between Ultragenyx Europe GmbH and Rentschler Biopharma SE

Commercial Master Service Agreement –

Drug Product, effective February 22, 2021, between Ultragenyx Pharmaceutical Inc.

Amendment No.

13 to Collaboration and License Agreement, effective as of May 16, 2023, between Ultragenyx Pharmaceutical Inc.

and Kyowa Kirin Co., Ltd.

Unit Purchase Agreement, dated as of July 15, 2022, by and among Ultragenyx Pharmaceutical Inc., GeneTx Biotherapeutics LLC, the Unitholders and Deborah A.

Commercial Supply and Services Agreement – Drug Substance, effective December 7, 2017, between Ultragenyx Europe GmbH and Rentschler Biopharma SE

Commercial Master Service Agreement – Drug Product, effective February 22, 2021, between Ultragenyx Pharmaceutical Inc.

and BSP Pharmaceuticals S.p.A

Supply Agreement, dated as of November 19, 2012, between Ultragenyx Pharmaceutical Inc.

and CREMER OLEO GmbH & Co KG

Master Services Agreement, dated April 8, 2019, between Ultragenyx Pharmaceutical Inc.

and Aenova Haupt Pharma Wolfratshausen GmbH

Commercial Supply Agreement, dated June 19, 2023, between Ultragenyx Pharmaceutical Inc.

and IOI Oleo GmbH

Royalty Purchase Agreement, dated as of December 17, 2019, between Ultragenyx Pharmaceutical Inc.

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and OCM LS23 Holdings LP

Unit Purchase Agreement, dated as of July 15, 2022, by and among Ultragenyx Pharmaceutical Inc., GeneTx Biotherapeutics LLC, the Unitholders and Deborah A.

2011 Equity Incentive Plan (including forms of Stock Option Grant Notice and Stock Option Agreement thereunder)

Amendment to the 2011 Equity Incentive Plan

2014 Incentive Plan (as amended)

Form of Incentive Stock Option Agreement

Form of Non Statutory Stock Option Agreement (Employees)

Form of Non Statutory Stock Option Agreement (Employees)(ex-U.S.)

Form of Restricted Stock Unit Agreement (Employees)

Form of Restricted Stock Unit Agreement (Employees)(ex-U.S.)

Form of Non-Statutory Stock Option Agreement (Annual Grant for Directors)

Form of Restricted Stock Unit Agreement (Annual Grant for Directors)

Form of Non-Statutory Stock Option Agreement (Grant for New Directors)

Form of Restricted Stock Unit Agreement (Grant for New Directors)

Form of Incentive Stock Option Agreement (2014 Plan)

Form of Non Statutory Stock Option Agreement (Employees) (2014 Plan)

Form of Restricted Stock Unit Agreement (Employees) (2014 Plan )

Form of Non-Statutory Stock Option Agreement (Annual Grant for Directors) (2014 Plan)

Form of Restricted Stock Unit Agreement (Annual Grant for Directors ) (2014 Plan)

Form of Non-Statutory Stock Option Agreement (Grant for New Directors) (2014 Plan)

Form of Restricted Stock Unit Agreement (Grant for New Directors) (2014 Plan)

2023 Incentive Plan

Form of Incentive Stock Option Agreement (2023 Plan)

Form of Non Statutory Stock Option Agreement (Employees)(2023 Plan)

Form of Restricted Stock Unit Agreement (Employees)(2023 Plan)

Form of Non-Statutory Stock Option Agreement (Annual Grant for Directors) (2023 Plan)

Form of Restricted Stock Unit Agreement (Annual Grant for Directors) (2023 Plan)

Form of Non-Statutory Stock Option Agreement (Grant for New Directors)(2023 Plan)

Form of Restricted Stock Unit Agreement (Grant for New Directors) (2023 Plan)

Form of Performance Stock Unit Agreement (2022)

Form of Performance Stock Unit Agreement (2023)

2014 Employee Stock Purchase Plan (as amended)

Amended and Restated 2014 Employee Stock Purchase Plan

Corporate Bonus Plan

Employment Inducement Plan

First Amendment to Employment Inducement Plan

Form of Non Statutory Stock Option Agreement (Inducement Plan)

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Amendment, dated September 13, 2022, to Offer Letter between Ultragenyx Pharmaceutical Inc.

Offer Letter, dated as of January 15, 2018, between Ultragenyx Pharmaceutical Inc.

and Camille Bedrosian, M.D.

Amendment, dated September 13, 2022, to Offer Letter between Ultragenyx Pharmaceutical Inc.

and Camille Bedrosian, M.D.

Amended and Restated Offer Letter, dated March 31, 2023, between Ultragenyx Pharmaceutical Inc.

and Eric Crombez, M.D.

Offer Letter, dated June 2, 2023, between Ultragenyx Pharmaceutical Inc.

and Howard Horn

Amendment, dated September 6, 2023, to the Offer Letter between Ultragenyx Pharmaceutical Inc.

and Howard Horn

Offer Letter, dated May 16, 2017, between Ultragenyx Pharmaceutical Inc.

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Lease Agreement, dated as of December 8, 2015, between Marina Boulevard Property, LLC and Ultragenyx Pharmaceutical Inc.

Indenture of Lease, dated March 11, 2014, between Dimension Therapeutics, Inc.

and Rivertech Associates II, LLC

Second Lease Amendment, dated April 28, 2017, to the Lease between Dimension Therapeutics, Inc.

and Rivertech Associates II, LLC

Third Lease Amendment, dated December 31, 2018, to the Lease between Ultragenyx Pharmaceutical Inc.

and Rivertech Associates II, LLC

Lease Agreement, dated November 2, 2015, between Dimension Therapeutics, Inc.

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Power of Attorney (included on the signature page of this report)

Certification of Principal Executive Officer and Principal Financial Officer of Ultragenyx Pharmaceutical Inc., as required by Rule 13a-14(a) or Rule 15d-14(a) of the Exchange Act as adopted pursuant to Section 302 of the Sarbanes-Oxley Act of 2002

Certification of Principal Executive Officer of Ultragenyx Pharmaceutical Inc., as required by Rule 13a-14(a) or Rule 15d-14(a) of the Exchange Act as adopted pursuant to Section 302 of the Sarbanes-Oxley Act of 2002

Certification of Principal Financial Officer of Ultragenyx Pharmaceutical Inc., as required by Rule 13a-14(a) or Rule 15d-14(a) of the Exchange Act as adopted pursuant to Section 302 of the Sarbanes-Oxley Act of 2002

Certification by the Principal Executive Officer and Principal Financial Officer, as required by Rule 13a-14(b) or Rule 15d-14(b) and Section 1350 of Chapter 36 of Title 18 of the United States Code (18 U.S.C.

Ultragenyx Pharmaceutical Inc.

Clawback Policy

XBRL Instance Document, formatted in Inline XBRL

Inline XBRL Taxonomy Extension Schema Document

Inline XBRL Taxonomy Extension Calculation Linkbase Document

Inline XBRL Taxonomy Extension Definition Linkbase Document

Inline XBRL Taxonomy Extension Labels Linkbase Document

Inline XBRL Taxonomy Extension Presentation Linkbase Document

The cover page from this Annual Report on Form 10-K, formatted in Inline XBRL

The cover page from this Annual Report on Form 10-K, formatted in Inline XBRL and contained in Exhibit 101

* Certain identified information has been omitted by means of marking such information with asterisks in reliance on Item 601(b)(10)(iv) of Regulation S-K because it is both (i) not material and (ii) the type that the registrant treats as private or confidential.

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President and Chief Executive Officer

(Principal Executive Officer and Principal Financial Officer)

(Principal Executive Officer)

February 21, 2024

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KNOW ALL PERSONS BY THESE PRESENTS, that each person whose signature appears below constitutes and appoints Emil D.

Kakkis, M.D., Ph.D., as his or her true and lawful attorneys-in-fact and agents, with full power of substitution for him or her, and in his or her name in any and all capacities, to sign any and all amendments to this Annual Report, and to file the same, with exhibits thereto and other documents in connection therewith, with the Securities and Exchange Commission, granting unto said attorneys-in-fact and agents, and each of them, full power and authority to do and perform each and every act and thing requisite and necessary to be done therewith, as fully to all intents and purposes as he or she might or could do in person, hereby ratifying and confirming all that said attorneys-in-fact and agents, and any of them, his or her substitute or substitutes, may lawfully do or cause to be done by virtue hereof.

Kakkis, M.D., Ph.D.

and Howard Horn, and each of them, as his or her true and lawful attorneys-in-fact and agents, with full power of substitution for him or her, and in his or her name in any and all capacities, to sign any and all amendments to this Annual Report, and to file the same, with exhibits thereto and other documents in connection therewith, with the Securities and Exchange Commission, granting unto said attorneys-in-fact and agents, and each of them, full power and authority to do and perform each and every act and thing requisite and necessary to be done therewith, as fully to all intents and purposes as he or she might or could do in person, hereby ratifying and confirming all that said attorneys-in-fact and agents, and any of them, his or her substitute or substitutes, may lawfully do or cause to be done by virtue hereof.

Pursuant to the requirements of the Securities Exchange Act of 1934, this report has been signed below by the following persons on behalf of the registrant and in the capacities and on the dates indicated.

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President and Chief Executive Officer and Director

(Principal Executive Officer and Principal Financial Officer)

(Principal Executive Officer)

February 21, 2024

/s/ Howard Horn

Executive Vice President, Chief Financial Officer, Corporate Strategy

(Principal Financial Officer)

February 21, 2024

/s/ Theodore A.

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February 21, 2024

/s/ Lars Ekman

Lars Ekman, M.D., Ph.D.

February 16, 2023

/s/ Matthew K.

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February 21, 2024

/s/ Corsee D.

Sanders, Ph.D.

February 16, 2023

/s/ Amrit Ray, M.D.

/s/ Amrit Ray

February 21, 2024

Amrit Ray, M.D.

/s/ Corsee D.

February 21, 2024

Sanders, Ph.D.

/s/ Shehnaaz Suliman

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Consolidated Statements of Comprehensive Loss

Consolidated Statements of Stockholders’

Consolidated Statements of Stockholders’ Equity

Consolidated Statements of Cash Flows

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We have audited the accompanying consolidated balance sheets of Ultragenyx Pharmaceutical Inc.

(the Company) as of December 31, 2022 and 2021, the related consolidated statements of operations, comprehensive loss, stockholders' equity and cash flows for each of the three years in the period ended December 31, 2022, and the related notes (collectively referred to as the “consolidated financial statements”).

(the Company) as of December 31, 2023 and 2022, the related consolidated statements of operations, comprehensive loss, stockholders' equity and cash flows for each of the three years in the period ended December 31, 2023, and the related notes (collectively referred to as the “consolidated financial statements”).

In our opinion, the consolidated financial statements present fairly, in all material respects, the financial position of the Company at December 31, 2023 and 2022, and the results of its operations and its cash flows for each of the three years in the period ended December 31, 2023, in conformity with U.S.

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These financial statements are the responsibility of the Company's management.

Our responsibility is to express an opinion on the Company’s financial statements based on our audits.

We are a public accounting firm registered with the PCAOB and are required to be independent with respect to the Company in accordance with the U.S.

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The Company estimates an imputed interest on the unamortized portion of the liability and records non-cash interest expense relating to the transaction.

Auditing the Company’s liabilities related to the sale of future royalties was complex due to the subjective judgments required to forecast the expected royalty payments subject to each agreement.

Specifically, the forecasted revenues of Crysvita involve significant estimation uncertainty given the limited historical Crysvita sales data.

How We Addressed the Matter in Our Audit

We obtained an understanding, evaluated the design and tested the operating effectiveness of controls over the Company’s process of accounting for the liabilities related to the sale of future royalties, including controls over the Company’s estimates of projected sales of Crysvita in the European and North American markets.

To test management’s estimates of the future royalties and the imputed effective interest rates, we performed audit procedures that included, among others, evaluating the reasonableness of management’s assumptions related to the treatable patient populations, estimated pricing and reimbursement, and the rate of adoption.

We compared the significant assumptions with historical trends of actual sales, analyst expectations and performed sensitivity analyses of estimated future royalties to evaluate the changes in the future royalties on the implied effective interest rates.

/s/ Ernst & Young LLP

We have served as the Company’s auditor since 2010.

We have served as the Company’s auditor since 2012.

San Mateo, California

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Accounts receivable, net

Prepaid expenses and other current assets

Total current assets

Property, plant, and equipment, net

Equity investments

Marketable debt securities

Right-of-use assets

Intangible assets, net

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Lease liabilities

Liabilities for sales of future royalties

Total current liabilities

Contract liabilities

Lease liabilities

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Commitments and contingencies (Notes 9 and 15)

Stockholders’

Preferred stock, par value of $ 0.001 per share—

25,000,000 shares authorized;

outstanding as of December 31, 2022 and December 31, 2021

Common stock, par value of $ 0.001 per share—

250,000,000 shares authorized;

70,197,297 and 69,344,998 shares issued and outstanding as of December 31, 2022

and December 31, 2021, respectively

Stockholders’ equity:

Preferred stock, par value of $ 0.001 per share— 25,000,000 shares authorized;

outstanding in 2023 and in 2022

Common stock, par value of $ 0.001 per share— 250,000,000 shares authorized;

outstanding— 82,315,590 in 2023 and 70,197,297 in 2022

Treasury stock, at cost, 9,559 in 2023 and nil in 2022

Deferred compensation obligation

Additional paid-in capital

Accumulated other comprehensive loss

Accumulated other comprehensive income (loss)

Accumulated deficit

Total stockholders’

Total liabilities and stockholders’

Total stockholders’ equity

Total liabilities and stockholders’ equity

See accompanying notes.

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Year Ended December 31,

Collaboration and license

Product sales

Non-cash collaboration royalty revenue

Royalty revenue

Collaboration and license

Total revenues

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Non-cash interest expense on liabilities for sales of future royalties

Other income (expense)

Other expense

Loss before income taxes

Provision for income taxes

Benefit from (provision for) income taxes

Net loss per share, basic and diluted

Weighted-average shares used in computing net loss per share, basic and diluted

Shares used in computing net loss per share, basic and diluted

See accompanying notes.

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ULTRAGENYX PHARMACEUTICAL INC.

CONSOLIDATED STATE MENTS OF STOCKHOLDERS’

CONSOLIDATED STATE MENTS OF STOCKHOLDERS’ EQUITY

(In thousands, except share amounts)

Comprehensive

Deferred Compensation

Stockholders'

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Balance as of December 31, 2020

Issuance of common stock in connection with underwritten

public offering, net of issuance costs

Issuance of common stock in connection with license agreement,

net of issuance costs

Issuance of common stock in connection with at-the-market

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Stock-based compensation

Issuance of common stock upon exercise of warrants and under

Issuance of common stock under

equity plan awards, net of tax

Other comprehensive income

Other comprehensive loss

Balance as of December 31, 2021

Issuance of common stock in connection with at-the-market

offering, net of issuance costs

Stock-based compensation

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Balance as of December 31, 2022

Issuance of common stock and pre-funded warrants in connection with underwritten

public offering, net of issuance costs

Issuance of common stock in connection with

at-the-market offering, net of issuance costs

Stock-based compensation

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equity plan awards, net of tax

Other comprehensive loss

Deferred compensation

Other comprehensive income

Balance as of December 31, 2023

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Accounts receivable

Prepaid expenses and other assets

Accounts payable, accrued, and other liabilities

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Purchase of marketable debt securities

Purchase of equity investments

Proceeds from sale of marketable debt securities

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Payment for intangible asset

Net cash used in investing activities

Net cash provided by (used in) investing activities

Financing activities:

Proceeds from the sale of future royalties, net

Proceeds from the issuance of common stock in connection with underwritten

public offerings, net

Proceeds from the issuance of common stock in connection with the license

agreement, net

Proceeds from the issuance of common stock and pre-funded warrants in connection with underwritten

public offerings, net of issuance costs

Proceeds from the issuance of common stock in connection with at-the-market

offering, net

offering, net of issuances costs

Proceeds from the issuance of common stock from exercise of warrants and equity

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Effect of exchange rate changes on cash

Net (decrease) increase in cash, cash equivalents, and restricted cash

Net increase (decrease) in cash, cash equivalents, and restricted cash

Cash, cash equivalents, and restricted cash at beginning of year

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Supplemental disclosures of non-cash investing and financing information:

Acquired lease liabilities arising from obtaining right-of-use assets

Stock-based compensation capitalized into ending inventory

Acquired lease liabilities arising from obtaining right-of-use assets and property, plant, and equipment

Costs of property, plant and equipment included in accounts payable, accrued, and other liabilities

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Ultragenyx Pharmaceutical Inc., or the Company, is a biopharmaceutical company incorporated in Delaware.

The Company is focused on the identification, acquisition, development, and commercialization of novel products for the treatment of serious rare and ultra-rare genetic diseases.

The Company is focused on the identification, acquisition, development, and commercialization of novel products for the treatment of serious rare and ultrarare genetic diseases.

The Company operates as one reportable segment and has four commercially approved products.

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and the European Economic Area, or EEA, for the treatment of homozygous familial hypercholesterolemia, or HoFH.

In January 2022, the Company licensed exclusive rights from Regeneron Pharmaceuticals, or Regeneron, to commercialize Evkeeza® (evinacumab) outside of the U.S.

The Company has exclusive rights to commercialize Evkeeza® (evinacumab) outside of the U.S.

In addition to the approved products, the Company has the following ongoing clinical development programs:

• UX111 (formerly ABO-102) is an AAV9 gene therapy product candidate for the treatment of patients with Sanfilippo syndrome type A, or MPS IIIA, a rare lysosomal storage disease;

In May 2022, the Company announced an exclusive license agreement with Abeona Therapeutics Inc., or Abeona, for UX111 whereby the Company assumed responsibility for the UX111 program, as further described in Note 8;

• DTX401 is an adeno-associated virus 8, or AAV8, gene therapy product candidate for the treatment of patients with glycogen storage disease type Ia, or GSDIa;

• DTX301 is an AAV8 gene therapy product candidate in development for the treatment of patients with ornithine transcarbamylase, or OTC deficiency, the most common urea cycle disorder;

UX143 (setrusumab), which is subject to the Company ’

s collaboration agreement with Mereo BioPharma 3, or Mereo, is a fully human monoclonal antibody that inhibits sclerostin, a protein that acts on a key bone-signaling pathway and inhibits the activity of bone-forming cells for the treatment of patients with osteogenesis imperfect, or OI;

GTX-102 is an antisense oligonucleotide, or ASO, which the Company is developing through GeneTx Biotherapeutics LLC, or GeneTx, for the treatment of Angelman syndrome, a debilitating and rare neurogenetic disorder caused by loss-of-function of the maternally inherited allele of the UBE3A gene.

In July 2022, the Company executed its option to acquire GeneTx as further described in Note 7;

• UX143 (setrusumab), which is subject to the Company ’ s collaboration agreement with Mereo BioPharma 3, or Mereo, is a fully human monoclonal antibody that inhibits sclerostin, a protein that acts on a key bone-signaling pathway and inhibits the activity of bone-forming cells for the treatment of patients with osteogenesis imperfect, or OI;

• GTX-102 is an antisense oligonucleotide, or ASO for the treatment of Angelman syndrome, a debilitating and rare neurogenetic disorder caused by loss-of-function of the maternally inherited allele of the UBE3A gene.;

• UX701 is an adeno-associated virus 9, or AAV9, gene therapy designed to deliver stable expression of a truncated version of the ATP7B copper transporter following a single intravenous infusion to improve copper distribution and excretion from the body and reverse pathological findings of Wilson liver disease;

UX053 is a messenger RNA, or mRNA, product candidate designed for the treatment of patients with Glycogen Storage Disease Type III, or GSDIII, a disease caused by a glycogen debranching enzyme, or AGL, deficiency that results in glycogen accumulation in the liver and muscle.

The Company has sustained operating losses and expects such annual losses to continue over the next several years.

The Company’s ultimate success depends on the outcome of its research and development and commercialization activities.

Management recognizes that the Company will likely need to raise additional capital to fully implement its business plans.

The Company’s ultimate success depends on the outcome of its research and development and commercialization activities.

Through December 31, 2023 , the Company has relied primarily on its sale of equity securities, its revenues from commercial products, its sale of future royalties, and strategic collaboration arrangements to finance its operations.

ULTRAGENYX PHARMACEUTICAL INC.

Notes to Consolidated Financial Statements (continued)

The Company expects it will need to raise additional capital through the issuance of equity, borrowings, or strategic alliances with partner companies.

The Company may need to raise additional capital to fully implement its business plans through the issuance of equity, borrowings, or strategic alliances with partner companies.

However, if such financing is not available at adequate levels, the Company would need to reevaluate its operating plans.

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All intercompany balances and transactions have been eliminated.

ULTRAGENYX PHARMACEUTICAL INC.

Notes to Consolidated Financial Statements (continued)

Use of Estimates

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Cash equivalents consist primarily of amounts invested in money market accounts.

Restricted cash primarily consists of money market accounts used as collateral for the Company’s obligations under its facility leases and the gene therapy building construction project.

The following table provides a reconciliation of cash, cash equivalents, and restricted cash reported within the Consolidated Balance Sheets that sum to the total of the amounts shown in the Consolidated Statements of Cash Flows (in thousands):

Restricted cash primarily consists of money market accounts used as collateral for the Company’s obligations under its facility leases and the gene therapy building construction project.

The following table provides a reconciliation of cash, cash equivalents, and restricted cash reported within the Consolidated Balance Sheets that sum to the total of the same such amounts shown in the Consolidated Statements of Cash Flows (in thousands):

Cash and cash equivalents

Restricted cash included in prepaid expenses and other current assets

Restricted cash included in other assets

Restricted cash included in other current assets

Restricted cash included in other non-current assets

Total cash, cash equivalents, and restricted cash

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Marketable Debt Securities

All marketable debt securities have been classified as “available-for-sale”

and are carried at estimated fair value as determined based upon quoted market prices or pricing models for similar securities.

All marketable debt securities have been classified as “available-for-sale” and are carried at estimated fair value as determined based upon quoted market prices or pricing models for similar securities.

Management determines the appropriate classification of its investments at the time of purchase and reevaluates such designation as of each balance sheet date.

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Equity securities with no readily determinable fair values are recorded using the measurement alternative of cost adjusted for observable price changes in orderly transactions for identical or similar investments of the same issuer less impairment, if any.

Investments in equity securities are recorded in Equity investments on the Company's Consolidated

Investments in equity securities are recorded in Equity investments on the Company's Consolidated Balance Sheets.

Unrealized gains and losses are reported in Change in fair value of equity investments on the Company’s Consolidated Statements of Operations.

The Company regularly reviews its non-marketable equity securities for indicators of impairment.

ULTRAGENYX PHARMACEUTICAL INC.

Notes to Consolidated Financial Statements (continued)

Balance Sheets.

Unrealized gains and losses are reported in Change in fair value of equity investments on the Company’s Consolidated Statements of Operations.

The Company regularly reviews its non-marketable equity securities for indicators of impairment.

Concentration of Credit Risk, Credit Losses, and Other Risks and Uncertainties

Financial instruments that potentially subject the Company to a concentration of credit risk consist of cash, cash equivalents, and investments.

The Company’s cash, cash equivalents, and investments are held by financial institutions that management believes are of high credit quality.

The Company’s investment policy limits investments to fixed income securities denominated and payable in U.S.

The Company’s cash, cash equivalents, and investments are held by financial institutions that management believes are of high credit quality.

The Company’s investment policy limits investments to fixed income securities denominated and payable in U.S.

dollars such as U.S.

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The Company is exposed to credit risk in the event of default by the financial institutions holding its cash and cash equivalents, corporate issuers, and other financial instruments, to the extent recorded in the Consolidated Balance Sheets.

For trade receivables and other instruments, the Company uses a new forward-looking expected loss model that generally results in the earlier recognition of allowances for losses.

For available-for-sale debt securities with unrealized losses, the losses are recognized as allowances rather than as reductions in the amortized cost of the securities.

The Company is exposed to credit losses primarily through receivables from customers and collaborators and through its available-for-sale debt securities.

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For available-for-sale debt securities with unrealized losses, the losses are recognized as allowances rather than as reductions in the amortized cost of the securities.

The Company’s expected loss allowance methodology for the receivables is developed using historical collection experience, current and future economic market conditions, a review of the current aging status and financial condition of the entities.

Specific allowance amounts are established to record the appropriate allowance for customers that have a higher probability of default.

Balances are written off when determined to be uncollectible.

credit ratings and any changes in those ratings, as well as reviewing current and future economic market conditions and the issuers’

current status and financial condition.

The Company’s expected loss allowance methodology for the debt securities is developed by reviewing the extent of the unrealized loss, the size, term, geographical location, and industry of the issuer, the issuers’ credit ratings and any changes in those ratings, as well as reviewing current and future economic market conditions and the issuers’ current status and financial condition.

There was no allowance for losses on available-for-sale debt securities which were attributable to credit risk for the years ended December 31, 2023 and 2022.

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Depreciation and amortization is computed using the straight-line method over the estimated useful lives of the respective assets.

Depreciation and amortization begins at the time the asset is placed in service.

Interest costs incurred during the construction of major capital projects are capitalized until the underlying asset is ready to be placed in service, at which point the interest costs are amortized as depreciation expense over the life of the underlying asset.

Depreciation and amortization begins when the asset is placed in service.

Interest costs incurred during the construction of major capital projects are capitalized until the underlying asset is ready to be placed in service.

Maintenance and repairs are charged to operations as incurred.

Upon sale or retirement of assets, the cost and related accumulated depreciation or amortization are removed from the balance sheet and the resulting gain or loss, if any, is reflected in operations.

ULTRAGENYX PHARMACEUTICAL INC.

Notes to Consolidated Financial Statements (continued)

The useful lives of property, plant, and equipment are as follows:

Research and development equipment

Furniture and office equipment

Computer equipment and software

Not applicable

Leasehold improvements

Shorter of lease term or estimated useful life

Balance Sheet Components” for further disclosure on the useful lives of property, plant, and equipment.

Intangible Assets

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The Company measures fair value based on the estimated future undiscounted cash flows associated with these assets in addition to other assumptions and projections that the Company deems to be reasonable and supportable.

ULTRAGENYX PHARMACEUTICAL INC.

Notes to Consolidated Financial Statements (continued)

Indefinite-lived intangibles consist of acquired in-process research and development, or IPR&D.

IPR&D assets represent capitalized incomplete research projects that the Company acquired through business combinations.

Such assets are initially measured at their acquisition date fair values and are tested for impairment, until the completion or abandonment of the associated research and development efforts.

Such assets are initially measured at their acquisition date fair values and are tested for impairment annually and whenever events or changes in circumstances indicate that the carrying amount may not be recoverable.

When development of the project is complete, which generally occurs when regulatory approval to market a product is obtained, the associated assets will be deemed finite-lived and will be amortized over a period that best reflects the economic benefits provided by these assets.

The Company tests its indefinite-lived intangible assets for impairment annually during the fourth quarter and more frequently if events or changes in circumstances indicate that it is more likely than not that the asset is impaired.

If it is determined that an intangible asset becomes impaired, the carrying value is written down to its fair value with the related impairment charge recognized in Consolidated Statements of Operations in the period in which the impairment occurs.

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If the asset is considered to be impaired, the amount of any impairment is measured as the difference between the carrying value and the fair value of the impaired asset.

The Company has not recorded impairment of any long-lived assets.

The Company has not recorded material impairment of any long-lived assets.

Accruals of Research and Development Costs

The Company records accruals for estimated costs of research, preclinical and clinical studies and manufacturing development.

These costs are a significant component of the Company’s research and development expenses.

A substantial portion of the Company’s ongoing research and development activities are conducted by third-party service providers, including contract research organizations.

These costs are a significant component of the Company’s research and development expenses.

A substantial portion of the Company’s ongoing research and development activities are conducted by third-party service providers, including contract research organizations.

The Company accrues the costs incurred under its agreements with these third parties based on actual work completed in accordance with agreements established with these third parties.

The Company determines the actual costs through obtaining information from external service providers as to the progress or stage of completion of the services and the agreed-upon fee to be paid for such services.

Revenue Recognition

Product Sales

The Company sells its approved products through a limited number of distributors.

Under ASC 606, revenue from product sales is recognized at the point in time when control is transferred to these distributors.

The Company also recognizes revenue from sales of certain products on a “named patient” basis, which are allowed in certain countries prior to the commercial approval of the product.

Prior to recognizing revenue, the Company makes estimates of the transaction price, including any variable consideration that is subject to a constraint.

Amounts of variable consideration are included in the transaction price to the extent that it is probable that a significant reversal in the amount of cumulative revenue recognized will not occur and when the uncertainty associated with the variable consideration is subsequently resolved.

Product sales are recorded net of estimated government-mandated rebates and chargebacks, estimated product returns, and other deductions.

Provisions for returns and other adjustments are provided for in the period the related revenue is recorded, as estimated by management.

These reserves are based on estimates of the amounts earned or to be claimed on the related sales and are reviewed periodically and adjusted as necessary.

The Company’s estimates of government mandated rebates, chargebacks, estimated product returns, and other deductions depends on the identification of key customer contract terms and conditions, as well as estimates of sales volumes to different classes of payors.

If actual results vary, the Company may need to adjust these estimates, which could have a material effect on earnings in the period of the adjustment.

ULTRAGENYX PHARMACEUTICAL INC.

Notes to Consolidated Financial Statements (continued)

Revenue Recognition

Collaboration and License Revenue

Collaboration, License, and Royalty Revenue

The Company has certain license and collaboration agreements that are within the scope of Accounting Standards Codification, or ASC, 808, Collaborative Agreements , which provides guidance on the presentation and disclosure of collaborative arrangements.

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The Company is considered an agent when the collaboration partner controls the product before transfer to the customers and has the ability to direct the use of and obtain substantially all of the remaining benefits from the product.

Funding received related to research and development services and commercialization costs is generally classified as a reduction of research and development expenses and selling, general and administrative expenses, respectively, in the Consolidated Statements of Operations, because the provision of such services for collaborative partners are not considered to be part of the Company’s ongoing major or central operations.

In order to record collaboration revenue, the Company utilizes certain information from its collaboration partners, including revenue from the sale of the product, associated reserves on revenue, and costs incurred for development and sales activities.

The Company utilizes certain information from its collaboration partners to record collaboration revenue, including revenue from the sale of the product, associated reserves on revenue, and costs incurred for development and sales activities.

For the periods covered in the financial statements presented, there have been no material changes to prior period estimates of revenues and expenses.

The Company also records royalty revenues under certain of the Company’s license or collaboration agreements in exchange for license of intellectual property.

If the Company does not have any future performance obligations for these license or collaboration agreements, royalty revenue is recorded as the underlying sales occur.

The Company sold the right to receive certain royalty payments from net sales of Crysvita in certain territories to RPI Finance Trust, or RPI, an affiliate of Royalty Pharma, and to OCM LS23 Holdings LP, an investment vehicle for Ontario Municipal Employees Retirement System, or OMERS, as further described in “Note 10.

Liabilities for Sales of Future Royalties”.

The Company records the royalty revenue from the net sales of Crysvita in the applicable territories on a prospective basis as non-cash royalty revenue in the Consolidated Statements of Operations over the term of the applicable arrangement.

The terms of the Company’s collaboration and license agreements may contain multiple performance obligations, which may include licenses and research and development activities.

The Company also records royalty revenues under certain of the Company’s license or collaboration agreements in exchange for license of intellectual property.

Liabilities for Sales of Future Royalties.” The Company records the royalty revenue from the net sales of Crysvita in the applicable territories on a prospective basis as non-cash royalty revenue in the Consolidated Statements of Operations over the term of the applicable arrangement.

The terms of the Company’s collaboration and license agreements may contain multiple performance obligations, which may include licenses and research and development activities.

The Company evaluates these agreements under ASC 606, Revenue from Contracts with Customers, or ASC 606, to determine the distinct performance obligations.

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The Company estimates the efforts needed to complete the performance obligations and recognizes revenue by measuring the progress towards complete satisfaction of the performance obligations using input measures.

Product Sales

The Company sells its approved products through a limited number of distributors.

Under ASC 606, revenue from product sales is recognized at the point in time when the delivery is made and when title and risk of loss transfers to these distributors.

The Company also recognizes revenue from sales of certain products on a “named patient”

basis, which are allowed in certain countries prior to the commercial approval of the product.

Prior to recognizing revenue, the Company makes estimates of the transaction price, including any variable consideration that is subject to a constraint.

Product sales are recorded net of estimated government-mandated rebates and chargebacks, estimated product returns, and other deductions.

Provisions for returns and other adjustments are provided for in the period the related revenue is recorded, as estimated by management.

These reserves are based on estimates of the amounts earned or to be claimed on the related sales and are reviewed

ULTRAGENYX PHARMACEUTICAL INC.

Notes to Consolidated Financial Statements (continued)

periodically and adjusted as necessary.

If actual results vary, the Company may need to adjust these estimates, which could have a material effect on earnings in the period of the adjustment.

Deferred Compensation Plan

The Company maintains a nonqualified deferred compensation plan whereby certain employees and members of the board of directors are able to defer certain equity awards and other compensation.

Amounts deferred are invested into shares of the Company's common stock, mutual funds, and other investment options.

The plan complies with the provisions of Section 409A of the Internal Revenue Code.

All of the various mutual funds held in the plan are classified as trading securities and recorded at fair value in other non-current assets in the Consolidated Balance Sheets with changes in fair value recognized as earnings in the period they occur.

The short-term portion of the corresponding liability for the plan is included in accrued expenses.

The long-term portion of the liability is included in other non-current liabilities in the Consolidated Balance Sheets.

Certain equity awards deferred under the plan are required to be settled through the issuance of Company stock.

These awards are recorded as treasury stock and deferred compensation obligation within stockholders’ equity.

Lease agreements are evaluated to determine whether an arrangement is or contains a lease in accordance with ASC 842, Leases .

The Company determines if an arrangement includes a lease at inception.

Right-of-use lease assets and lease liabilities are recognized based on the present value of the future minimum lease payments over the lease term at the commencement date.

Right-of-use lease assets and lease liabilities are

ULTRAGENYX PHARMACEUTICAL INC.

Notes to Consolidated Financial Statements (continued)

recognized based on the present value of the future minimum lease payments over the lease term at the commencement date.

The right-of-use lease asset includes any lease payments made and excludes lease incentives.

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The Company has elected to not separate lease and non-lease components.

See “Note 9.

Leases”

for further disclosure.

Leases” for further disclosure.

Comprehensive Loss

Comprehensive loss is the change in stockholders’

equity from transactions and other events and circumstances other than those resulting from investments by stockholders and distributions to stockholders.

The Company’s other comprehensive loss is comprised of unrealized gains and losses on investments in available-for-sale securities and foreign currency translation adjustments.

Comprehensive loss is the change in stockholders’ equity from transactions and other events and circumstances other than those resulting from investments by stockholders and distributions to stockholders.

The Company’s other comprehensive loss is comprised of unrealized gains and losses on investments in available-for-sale securities and foreign currency translation adjustments.

Research and Development

Research and development costs are expensed as incurred and consist of salaries and benefits, stock-based compensation expense, lab supplies and facility costs, as well as fees paid to other nonemployees and entities that conduct certain research and development activities on the Company’s behalf.

Amounts incurred in connection with license agreements are also included in research and development expense.

2 unchanged sentences

Stock-Based Compensation

Stock-based awards issued to employees, including stock options, performance stock options, or PSOs, restricted stock units, or RSUs, and performance stock units, or PSUs are recorded at fair value as of the grant date and recognized as expense on a straight-line basis over the employee’s requisite service period (generally the vesting period).

PSOs and PSUs vest only if certain specified criteria are achieved and the employees’

continued service requirements are met;

PSOs and PSUs vest only if certain specified criteria are achieved and the employees’ continued service requirements are met;

therefore, the expense recognition occurs when the likelihood of the PSOs and PSUs being earned is deemed probable.

Stock compensation expense on awards expected to vest are recognized net of estimated forfeitures.

Stock compensation expense on awards expected to vest is recognized net of estimated forfeitures.

The Company uses the liability method of accounting for income taxes.

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A valuation allowance is provided when it is more likely than not that some portion or all of a deferred tax asset will not be realized.

Due to the Company’s lack of earnings history, the net deferred tax assets have been fully offset by a valuation allowance.

In conjunction with the acquisition of Dimension Therapeutics, Inc., or Dimension, a deferred tax liability was recorded reflecting the tax impact of the difference between the book basis and tax basis of acquired IPR&D.

Such deferred income tax liability is not used to offset deferred tax assets when analyzing the Company’s valuation allowance as the acquired IPR&D is considered to have an indefinite life until the Company completes or abandons development of the acquired IPR&D.

ULTRAGENYX PHARMACEUTICAL INC.

Notes to Consolidated Financial Statements (continued)

The Company recognizes benefits of uncertain tax positions if it is more likely than not that such positions will be sustained upon examination based solely on their technical merits, as the largest amount of benefit that is more likely than not to be realized upon the ultimate settlement.

The Company’s policy is to recognize interest and penalties related to the underpayment of income taxes as a component of income tax expense or benefit.

To date, there have been no interest or penalties charged in relation to the unrecognized tax benefits.

ULTRAGENYX PHARMACEUTICAL INC.

Notes to Consolidated Financial Statements (continued)

Foreign Currency

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Basic net loss per share is calculated by dividing the net loss by the weighted-average number of shares of common stock outstanding during the period, without consideration for common stock equivalents.

Shares of common stock into which pre-funded warrants may be exercised are considered outstanding for the purposes of computing basic net loss per share because the shares may be issued for little or no consideration, are fully vested and are exercisable after the original issuance date.

Diluted net loss per share is the same as basic net loss per share, since the effects of potentially dilutive securities are antidilutive.

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The authoritative guidance on fair value measurements establishes a three-tier fair value hierarchy for disclosure of fair value measurements as follows:

Level 1 —Inputs are unadjusted, quoted prices in active markets for identical assets or liabilities at the measurement date;

Level 2 —Inputs are observable, unadjusted quoted prices in active markets for similar assets or liabilities, unadjusted quoted prices for identical or similar assets or liabilities in markets that are not active, or other inputs that are observable or can be corroborated by observable market data for substantially the full term of the related assets or liabilities;

Level 3 —Unobservable inputs that are significant to the measurement of the fair value of the assets or liabilities that are supported by little or no market data.

The Company’s financial instruments consist of Level 1, Level 2, and Level 3 assets.

Level 1 —Inputs are unadjusted, quoted prices in active markets for identical assets or liabilities at the measurement date;

Level 3 —Unobservable inputs that are significant to the measurement of the fair value of the assets or liabilities that are supported by little or no market data.

The Company’s financial instruments consist of Level 1, Level 2, and Level 3 assets.

Where quoted prices are available in an active market, securities are classified as Level 1.

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Where applicable these models project future cash flows and discount the future amounts to a present value using market-based observable inputs obtained from various third-party data providers, including but not limited to, benchmark yields, interest rate curves, reported trades, broker/dealer quotes and reference data.

The Company determines the fair value of its equity investments in Arcturus Therapeutics Holdings Inc., or Arcturus, and Solid Biosciences, Inc., or Solid, by using the quoted market prices, which are Level 1 fair value measurements.

The following tables set forth the fair value of the Company’s financial assets remeasured on a recurring basis based on the three-tier fair value hierarchy (in thousands):

The Company determines the fair value of its equity investments in Solid Biosciences, Inc., or Solid, by using the quoted market prices, which are Level 1 fair value measurements.

ULTRAGENYX PHARMACEUTICAL INC.

Notes to Consolidated Financial Statements (continued)

The following tables set forth the fair value of the Company’s financial assets remeasured on a recurring basis based on the three-tier fair value hierarchy (in thousands):

December 31, 2023

1 unchanged sentence

Money market funds

Certificates of deposits and time deposits

Certificates of deposit and time deposits

Corporate bonds

2 unchanged sentences

Government Treasury and agency securities

Debt securities in government-sponsored entities

Investment in Solid common stock

Deferred compensation assets

Total financial assets

Financial Liabilities:

Deferred compensation liabilities

December 31, 2022

1 unchanged sentence

Money market funds

Certificates of deposits and time deposits

Certificates of deposit and time deposits

Corporate bonds

3 unchanged sentences

Debt securities in government-sponsored entities

Investments in Arcturus and Solid common stock

Investment in Solid common stock

Deferred compensation assets

Total financial assets

Financial Liabilities:

Deferred compensation liabilities

Deferred compensation assets are recorded at fair value in other non-current assets in the Consolidated Balance Sheets.

There have been no significant gains or losses on deferred compensation assets for the periods presented.

Deferred compensation liabilities consist of short-term liabilities of $ 0.2 million and nil as of December 31, 2023 and 2022 , respectively, included in accrued liabilities on the Consolidated Balance Sheets, and long-term liabilities of $ 10.1 million and $ 4.7 million as of December 31, 2023 and 2022 , respectively, included in other non-current liabilities on the Consolidated Balance Sheets.

ULTRAGENYX PHARMACEUTICAL INC.

Notes to Consolidated Financial Statements (continued)

Balance Sheet Components

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Government Treasury and agency securities

Debt securities in government-sponsored entities

ULTRAGENYX PHARMACEUTICAL INC.

Notes to Consolidated Financial Statements (continued)

December 31, 2022

10 unchanged sentences

There have been no significant realized gains or losses on available-for-sale securities for the periods presented.

The unrealized losses on the Company’s investments in marketable debt securities were caused by increases in market yields on these investments.

The contractual terms of these investments do not permit the issuers to settle the securities at a price less than the par value.

Accordingly, it is expected that the securities will not be settled at a price less than the amortized cost basis of these investments.

The Company does not intend to sell the investments and it is not more likely than not that the Company will be required to sell the investments before recovery of their amortized cost basis.

Inventory consists of the following (in thousands):

1 unchanged sentence

Finished goods

Total inventory

ULTRAGENYX PHARMACEUTICAL INC.

Notes to Consolidated Financial Statements (continued)

Property, Plant, and Equipment, net

Property, plant, and equipment, net consists of the following (in thousands):

Useful life (years)

Leasehold improvements

Shorter of lease term or

estimated useful life

Research and development equipment

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Computer equipment and software

Manufacturing equipment

Not applicable

Construction-in-progress

Not applicable

Varies by asset

Property, plant, and equipment, gross

3 unchanged sentences

Amortization of leasehold improvements and software is included in depreciation expense.

The construction-in-progress balance primarily relates to the construction costs for the gene therapy manufacturing plant in Bedford, Massachusetts.

ULTRAGENYX PHARMACEUTICAL INC.

Notes to Consolidated Financial Statements (continued)

Construction in progress reflects amounts incurred for construction or improvements of property or costs for equipment that has not been placed in service.

The construction-in-progress balance as of December 31, 2022 is primarily the construction costs for the gene therapy manufacturing facility in Bedford, Massachusetts.

Accrued Liabilities

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Payroll and related expenses

Total accrued liabilities

Intangible Assets, net

2 unchanged sentences

IPR&D assets represent the fair value of acquired programs to develop an AAV gene therapy for OTC deficiency and to develop an AAV gene therapy for glycogen storage disease type Ia.

The fair value of IPR&D assets acquired was determined based on the discounted present value of each research project’s projected cash flows using an income approach, including the application of probability factors related to the likelihood of success of the program reaching final development and commercialization.

Additionally, the projections consider the relevant market sizes and growth factors, estimated future cash flows from product sales resulting from completed products and in-process projects and timing and costs to complete the in-process projects.

2 unchanged sentences

Finite-lived Intangibles

ULTRAGENYX PHARMACEUTICAL INC.

Notes to Consolidated Financial Statements (continued)

Subsequent to the FDA approval of Dojolvi for the treatment of LC-FAOD in 2020, the Company recorded $ 4.8 million for the attainment of various development and commercial milestones as finite-lived intangible assets which are amortized over a weighted-average useful life of 5.7 years.

1 unchanged sentence

Upon closing of the transaction in January 2022, the Company paid Regeneron a $ 30.0 million upfront payment.

As the upfront payment was related to the Company’s usage of intellectual property related to Evkeeza for HoFH, the upfront payment was recorded as an intangible asset, which is amortized over its useful life of 10.5 years.

During the year ended December 31, 2023, a $ 10.0 million regulatory milestone was achieved.

As both the upfront payment and the regulatory milestone are related to the Company’s use of intellectual property for Evkeeza for HoFH, these amounts were recorded as intangible assets, which are amortized over a weighted-average useful life of ten years .

The Company's intangible assets were as follows:

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The Company recorded costs of sales of $ 3.8 million, $ 3.2 million and $ 0.3 million for the years ended December 31, 2023, 2022, and 2021, respectively, related to the amortization of the intangible assets.

The expected amortization of the intangible assets, as of December 31, 2023, for each of the next five years and thereafter is as follows:

ULTRAGENYX PHARMACEUTICAL INC.

Notes to Consolidated Financial Statements (continued)

The expected amortization of the intangible assets, as of December 31, 2022, for each of the next five years and thereafter is as follows:

The following table disaggregates total revenues from external customers by collaboration and license revenue and product sales (in thousands):

The following table disaggregates total revenues from external customers by product sales, royalty revenue, and collaboration and license revenue (in thousands):

Year Ended December 31,

Product sales:

Total product sales

Crysvita royalty revenue

Collaboration and license revenue:

3 unchanged sentences

Total collaboration and license revenue

Product sales:

Total product sales

Crysvita non-cash collaboration royalty revenue

Total revenues

8 unchanged sentences

Balance of product sales reserve at end of year

ULTRAGENYX PHARMACEUTICAL INC.

Notes to Consolidated Financial Statements (continued)

The following table presents changes in the contract assets (liabilities) for the years ended December 31, 2022 and 2021 (in thousands):

The following table presents changes in the contract liabilities for the years ended December 31, 2023 and 2022 (in thousands):

Year Ended December 31,

1 unchanged sentence

Balance of contract liabilities at end of period, net

ULTRAGENYX PHARMACEUTICAL INC.

Notes to Consolidated Financial Statements (continued)

See Note 8 for additional details on contract liabilities activities.

The Company’s largest accounts receivable balance was from a collaboration partner and was 68 % and 71 % of the total accounts receivable balance as of December 31, 2022 and 2021 , respectively.

The Company’s largest accounts receivable balance was from a collaboration partner and was 53 % and 68 % of the total accounts receivable balance as of December 31, 2023 and 2022 , respectively.

GeneTx Acquisition

In August 2019, the Company entered into a Program Agreement and a Unitholder Option Agreement with GeneTx Biotherapeutics LLC, or GeneTx, to collaborate on the development of GeneTx’s GTX-102, an ASO for the treatment of Angelman syndrome.

Pursuant to the terms of the Unitholder Option Agreement, the Company made an upfront payment of $ 20.0 million for an exclusive option to acquire GeneTx, which was exercisable any time prior to 30 days following FDA acceptance of the IND for GTX-102.

Pursuant to the agreement, upon acceptance of the IND, which occurred in January 2020, the Company elected to extend the option period by paying an option extension payment of $ 25.0 million during the quarter ended March 31, 2020, which was recorded as an in-process research and development expense.

In April 2022, the parties entered into an amendment to the Unitholder Option Agreement, or the Amendment, which provided the Company with an additional, earlier option to acquire GeneTx for an option exercise price of $ 75.0 million based on the earlier of receipt of interim data in the Phase 1/2 study or a specified date, such option, the Interim Option.

During the exclusive option period, GeneTx was responsible for conducting the program based on the development plan agreed upon between the parties and, subject to the terms in the Program Agreement, had the decision-making authority on all matters in connection with the research, development, manufacturing and regulatory activities with respect to the Program.

In July 2022, the Company exercised the Interim Option to acquire GeneTx and entered into a Unit Purchase Agreement, or the Purchase Agreement, pursuant to which the Company purchased all the outstanding units of GeneTx.

In July 2022, pursuant to the terms of the Unitholder Option Agreement, as amended, the Company exercised the option to acquire GeneTx and entered into a Unit Purchase Agreement, or the Purchase Agreement, pursuant to which the Company purchased all the outstanding units of GeneTx.

In accordance with the terms of the Purchase Agreement, the Company paid the option exercise price of $ 75.0 million and an additional $ 15.6 million to acquire the outstanding cash of GeneTx, and adjustments for working capital and transaction expenses of $ 0.6 million, for a total purchase consideration of $ 91.2 million.

Additionally, the Company may make payments of up to $ 190.0 million upon the achievement of certain milestones, including up to $ 30.0 million in milestone payments upon achievement of the earlier of initiation of a Phase 3 clinical study or product approvals in Canada and the U.K., up to $ 85.0 million in additional regulatory approval milestones for the achievement of U.S.

The Company may be required to make payments of up to $ 190.0 million upon the achievement of certain milestones, including up to $ 30.0 million in milestone payments upon achievement of the earlier of initiation of a Phase 3 clinical study or product approvals in Canada and the U.K., up to $ 85.0 million in additional regulatory approval milestones for the achievement of U.S.

and EU product approvals, and up to $ 75.0 million in commercial milestone payments based on annual worldwide net product sales.

In addition, the Company will also pay tiered mid- to high single-digit percentage royalties based on licensed product annual net sales.

The Company will also pay tiered mid- to high single-digit percentage royalties based on licensed product annual net sales.

If the Company receives and resells an FDA priority review voucher, or PRV, in connection with a new drug application approval, GeneTx is entitled to receive a portion of proceeds from the sale or a cash payment from the Company if the Company choses to retain the PRV.

As part of the Company's acquisition of GeneTx, the Company assumed a License Agreement with Texas A&M University, or TAMU.

Under this agreement, TAMU is eligible to receive from the Company up to $ 23.5 million upon the achievement of various future milestones, a nominal annual license fee that may increase up to a maximum of $ 2.0 million, as well as royalties in the mid-single-digits of net sales.

The transaction was accounted as an asset acquisition, as substantially all of the fair value of the gross assets acquired was concentrated in a single identifiable in-process research and development intangible asset.

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Kyowa Kirin Co., Ltd.

In August 2013, the Company entered into a collaboration and license agreement with Kyowa Kirin Co., Ltd., or KKC (formerly Kyowa Hakko Kirin Co., Ltd.

In August 2013, the Company entered into a collaboration and license agreement with Kyowa Kirin Co., Ltd., or KKC.

Under the terms of this collaboration and license agreement, as amended, the Company and KKC collaborate on the development and commercialization of Crysvita in the field of orphan diseases in the U.S.

and Canada, or the profit-share territory, and in the European Union, United Kingdom, and Switzerland, or the European territory, and the Company has

ULTRAGENYX PHARMACEUTICAL INC.

Notes to Consolidated Financial Statements (continued)

the right to develop and commercialize such products in the field of orphan diseases in Mexico and Central and South America, or Latin America.

and Canada, or the Profit-Share Territory, and in the European Union, United Kingdom, and Switzerland, or the European Territory, and the Company has the right to develop and commercialize such products in the field of orphan diseases in Mexico and Central and South America, or Latin America.

Development Activities

In the field of orphan diseases, and except for ongoing studies being conducted by KKC, the Company is the lead party for development activities in the profit-share territory and in the European territory until the applicable transition date.

The Company shares the costs for development activities in the profit-share territory and the European territory conducted pursuant to the development plan before the applicable transition date equally with KKC.

In April 2023, which is the transition date for the profit-share territory, KKC will become the lead party and be responsible for the costs of the development activities.

However, the Company will continue to share the costs of the studies commenced prior to the applicable transition date equally with KKC.

In the field of orphan diseases, except for ongoing studies being conducted by KKC, the Company was the lead party for development activities in the Profit-Share Territory and in the European Territory until the applicable transition date.

The Company shared the costs for development activities in the Profit-Share Territory and the European Territory conducted pursuant to the development plan before the applicable transition date equally with KKC.

In April 2023, which was the transition date for the Profit-Share Territory, KKC became the lead party and became responsible for the costs of the subsequent development activities.

However, the Company will continue to equally share in the costs of the studies with KKC that commenced prior to the applicable transition date.

The collaboration and license agreements are within the scope of ASC 808, which provides guidance on the presentation and disclosure of collaborative arrangements.

Collaboration Revenue Related to Sales in the Profit-share Territory

The Company and KKC share commercial responsibilities and profits in the profit-share territory until April 2023.

Under the collaboration agreement, KKC manufactures and supplies Crysvita for commercial use in the profit-share territory and charges the Company a transfer price of 35 % of net sales through December 31, 2022, and 30 % thereafter.

The remaining profit or loss after supply costs from commercializing products in the profit-share territory are shared between the Company and KKC on a 50 / 50 basis until April 2023.

In April 2023, commercialization responsibilities for Crysvita in the profit-share territory will transition to KKC and KKC will be responsible for the commercialization of Crysvita in the territory at and after April 2023.

Thereafter, the Company will be entitled to receive a tiered double-digit revenue share from the mid- 20 % range up to a maximum rate of 30 %.

In September 2022, the Company entered into an amendment to the collaboration agreement which clarified the scope of increased participation by KKC in support of the Company’s commercial activities prior to April 2023 and granted the Company the right to continue to support KKC in commercial field activities in the U.S.

Collaboration and Royalty Revenue for Sales in the Profit-Share Territory

The Company and KKC shared commercial responsibilities and profits in the Profit-Share Territory until April 2023.

Under the collaboration agreement, KKC manufactured and supplied Crysvita for commercial use in the Profit-Share Territory and charged the Company a transfer price of 30 % of net sales in 2023, and 35 % prior to December 31, 2022.

The remaining profit or loss after supply

ULTRAGENYX PHARMACEUTICAL INC.

Notes to Consolidated Financial Statements (continued)

costs from commercializing products in the Profit-Share Territory was shared between the Company and KKC on a 50 / 50 basis until April 2023.

In April 2023, commercialization responsibilities for Crysvita in the Profit-Share Territory transitioned to KKC.

Thereafter, the Company is entitled to receive a tiered double-digit revenue share from the mid- 20 % range up to a maximum rate of 30 %.

In 2022, the Company entered into an amendment to the collaboration agreement which granted the Company the right to continue to support KKC in commercial field activities in the U.S.

through April 2024, subject to the limitations and conditions set forth in the amendment.

As a result, KKC will continue to support the Company’s commercial field and marketing efforts through a cost share arrangement through April 2024, subject to the limits and conditions set forth in the amendment.

After April 2024, the Company’s rights to promote Crysvita in the U.S.

will be limited to medical geneticists and the Company will solely bear its expenses related to the promotion of Crysvita in the profit-share territory.

As KKC is the principal in the sale transaction with the customer, the Company recognizes a pro-rata share of collaboration revenue, net of transfer pricing, in the period the sale occurs.

The Company concluded that its portion of KKC’s sales in the profit-share territory is analogous to a royalty and therefore recorded its share as collaboration revenue, similar to a royalty.

The parties subsequently mutually agreed to extend the Company's right to continue to support KKC in commercial field activities in the U.S.

through December 31, 2024, and as a result, the Company will continue to support commercial field efforts in the U.S.

through a cost share arrangement through December 2024.

After December 31, 2024, the Company’s rights to promote Crysvita in the U.S.

will be limited to medical geneticists and the Company will solely bear its expenses for the promotion of Crysvita in the Profit-Share Territory.

As KKC was the principal in the sale transaction with the customer during the profit-share period, the Company recognized a pro-rata share of collaboration revenue, net of transfer pricing, in the period the sale occurs.

The Company concluded that its portion of KKC’s sales in the Profit-Share Territory prior to April 2023 was analogous to a royalty and therefore recorded its share as collaboration revenue, similar to a royalty.

Starting in April 2023, the Company began to record the royalty revenue as the underlying sales occur.

In July 2022, the Company sold to OMERS its right to receive 30 % of the future royalty payments due to the Company based on net sales of Crysvita in the U.S.

and Canada, subject to a cap, beginning in April 2023, as further described in Note 10.

Royalty Revenue Related to Sales in the European Territory

KKC has the commercial responsibility for Crysvita in the European territory.

In December 2019, the Company sold its right to receive royalty payments based on sales in the European territory to Royalty Pharma, effective January 1, 2020, as further described in “Note 10.

Liabilities for Sales of Future Royalties.”

Prior to the Company’s sale of the royalty, the Company received a royalty of up to 10 % on net sales in the European territory, which was recognized as the underlying sales occur.

Beginning in 2020, the Company records the royalty revenue as non-cash royalty revenues.

During the years ended December 31, 2021 and 2020, there was a change in estimate of the revenue reserves related to sales made prior to January 1, 2020, as a result of which, the Company recorded $ 0.2 million and $ 1.5 million, respectively, as royalty revenue in the European territory.

The Company’s share of collaboration and royalty revenue related to Crysvita was as follows (in thousands):

Year Ended December 31,

Company's share of revenue in profit-share territory

Royalty revenue in European territory

Non-cash royalty revenue in European territory

ULTRAGENYX PHARMACEUTICAL INC.

Notes to Consolidated Financial Statements (continued)

Product Revenue Related to Sales in Other Territories

The Company records this revenue as royalty revenue.

Product Sales Revenue for Other Territories

The Company is responsible for commercializing Crysvita in Latin America and Turkey.

The Company is considered the principal in these territories as the Company controls the product before it is transferred to the customer.

Accordingly, the Company records revenue on a gross basis related to the sale of Crysvita once the product is delivered and the risk and title of the product is transferred to the distributor.

The Company recorded product sales of $ 42.7 million, $ 21.4 million, and $ 10.4 million for the years ended December 31, 2022, 2021, and 2020, respectively, net of estimated product returns and other deductions.

Accordingly, the Company records revenue on a gross basis for the sale of Crysvita once the product is delivered and the risk and title of the product is transferred to the distributor.

KKC has the option to assume responsibility for commercialization efforts in Turkey from the Company, after a certain minimum period.

Under the collaboration agreement, KKC manufactures and supplies Crysvita, which is purchased by the Company for sales in its territories and is based on 35 % of the net sales through December 31, 2022 and 30 % thereafter.

Under the collaboration agreement, KKC manufactures and supplies Crysvita, which is purchased by the Company for sales in Latin American territories and charges the Company a transfer price of 30 % of net sales.

The transfer price on these sales was 35 % prior to December 31, 2022.

The Company also pays to KKC a low single-digit royalty on net sales in Latin America.

Cost Sharing Payments

Under the collaboration agreement, KKC and the Company share certain development and commercialization costs.

As a result, the Company was reimbursed for these costs and operating expenses were reduced as follows (in thousands):

Total Crysvita revenue was as follows (in thousands):

Year Ended December 31,

Revenue in profit-share territory:

Collaboration revenue

Royalty revenue

Non-cash royalty revenue

Total revenue in Profit-Share Territory

Product sales

Royalty revenue in European Territory

Non-cash royalty revenue in European Territories

Total Crysvita revenue

Royalty Revenue for Sales in the European Territory

KKC has the commercial responsibility for Crysvita in the European Territory.

In December 2019, the Company sold its right to receive royalty payments based on sales in the European Territory to Royalty Pharma, effective January 1, 2020, as further described in Note 10.

Prior to the Company’s sale of the royalty, the Company received a royalty of up to 10 % on net sales in the European Territory, which was recognized as the underlying sales occur.

Beginning in 2020, the Company records the royalty revenue as non-cash royalty revenues.

The Company records this revenue as royalty revenue.

ULTRAGENYX PHARMACEUTICAL INC.

Notes to Consolidated Financial Statements (continued)

Collaboration Cost Sharing and Payments

Under the collaboration agreement, KKC and the Company share certain development and commercialization costs and as a result, the Company was reimbursed for these costs and operating expenses were reduced.

Additionally, KKC is owed a transfer price fee and royalties on certain revenues and the Company recorded amounts owed to KKC in cost of sales.

These amounts were recognized in the Company’s Statements of Operations in connection with the collaboration agreement with KKC as follows (in thousands):

Year Ended December 31,

Research and development

Selling, general and administrative

Cost of sales

Collaboration Receivable and Payable

The Company had accounts receivable from KKC in the amount of $ 27.5 million and $ 20.2 million from profit-share revenue and royalties and other receivables recorded in prepaid expenses and other current assets of $ 6.4 million and $ 16.0 million and accrued liabilities of $ 3.1 million and $ 2.3 million from commercial and development activity reimbursements, as of December 31, 2022 and 2021, respectively.

The Company had accounts receivable from KKC in the amount of $ 39.2 million and $ 27.5 million from profit-share revenue and royalties and other receivables recorded in other current assets of $ 1.1 million and $ 6.4 million and accrued liabilities of $ 5.3 million and $ 3.1 million from commercial and development activity reimbursements, as of December 31, 2023 and 2022, respectively.

Saint Louis University

In November 2010, the Company entered into a license agreement with Saint Louis University, or SLU.

Under the terms of this license agreement, SLU granted the Company an exclusive worldwide license to make, have made, use, import, offer for sale, and sell therapeutics related to SLU’s beta-glucuronidase product for use in the treatment of human diseases.

The Company made a milestone payment of $ 0.1 million upon approval of Mepsevii for treatment of MPS 7.

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Under the terms of this license agreement, as amended, BRI exclusively licensed to the Company its territories for certain intellectual property related to Dojolvi (triheptanoin) for the treatment of LC-FAOD.

For the years ended December 31, 2022, 2021, and 2020 , the Company recorded $ 2.5 million, nil and $ 2.0 million, respectively, for the attainment of various development and commercial milestones as finite-lived intangible assets.

For the years ended December 31, 2023 and 2022 , the Company recorded nil and $ 2.5 million, respectively, for the attainment of various development and commercial milestones as finite-lived intangible assets.

The Company is obligated to make additional future payments of up to $ 7.5 million contingent upon attainment of various development and commercial milestones.

3 unchanged sentences

The Company will pay an annual fee and certain milestone fees per disease indication, low to mid- single-digit royalty percentages on net sales of licensed products, and milestone and sublicense fees owed by REGENX to its licensors, contingent upon the attainment of certain development activities as outlined in the agreement.

ULTRAGENYX PHARMACEUTICAL INC.

Notes to Consolidated Financial Statements (continued)

The Company also has an option and license agreement with REGENX under which the Company has an exclusive, sublicensable, worldwide license to make, have made, use, import, sell, and offer for sale licensed products to treat Wilson disease and CDKL5 deficiency.

For each disease indication, the Company is obligated to pay an annual maintenance fee of $ 0.1 million and up to $ 9.0 million upon achievement of various milestones, as well as mid- to high single-digit royalties on net sales of licensed products and mid- single-digit to low double-digit percentage sublicenses fees, if any.

In March 2020, the Company entered into a license agreement with REGENX, for an exclusive, sublicensable, worldwide license to REGENX’s NAV AAV8 and AAV9 vectors for the development and commercialization of gene therapy treatments for a rare metabolic disorder.

In return for these rights, the Company made an upfront payment of $ 7.0 million, which was recorded as an in-process research and development expense during the year ended December 31, 2020.

The Company will pay certain annual fees of $ 0.1 million, milestone payments of up to $ 14.0 million, and royalties on any net sales of products incorporating the licensed intellectual property that range from a high single-digit to low double-digit royalty.

In return for these rights, the Company made an upfront payment of $ 7.0 million.

The Company will pay certain

ULTRAGENYX PHARMACEUTICAL INC.

Notes to Consolidated Financial Statements (continued)

annual fees of $ 0.1 million, milestone payments of up to $ 14.0 million, and royalties on any net sales of products incorporating the licensed intellectual property that range from a high single-digit to low double-digit royalty.

Bayer HealthCare LLC

13 unchanged sentences

On a product-by-product basis, the Company is obligated to make development and regulatory milestone payments of up to $ 24.5 million, and commercial milestone payments of up to $ 45.0 million if certain milestones are achieved.

For the year ended December 31, 2021, the Company achieved a $ 1.0 million development milestone related to UX053, which was paid with a corresponding credit received from Arcturus for prior research and collaboration activities.

For the year ended December 31, 2021, the Company achieved a $ 1.0 million development milestone, which was paid with a corresponding credit received from Arcturus for prior research and collaboration activities.

The Company is also obligated to pay Arcturus royalties on any net sales of products incorporating the licensed intellectual property that may range from a mid- single-digit to low double-digit percentage.

Pursuant to the agreement, the Company incurred nil , nil , and $ 0.4 million for the years ended December 31, 2022, 2021, and 2020, respectively, in research and development expense for the funding of certain research services received from Arcturus.

There were no material expenses for this arrangement during the years ended December 31, 2023, 2022, and 2021.

In June 2019, the Company entered into an Equity Purchase Agreement and an amendment to the Research Collaboration and License Agreement, or License Agreement, to expand the field of use and increase the number of disease targets to include mRNA, DNA and siRNA therapeutics for up to 12 rare diseases.

Pursuant to the agreements, the Company paid $ 6.0 million in cash upfront to Arcturus and purchased 2,400,000 shares of Arcturus’

common stock at a stated value of $ 10.00 per share, resulting in a total of $ 30.0 million of consideration paid at the close of the transaction.

As a result, the Company received expanded license rights under the License Agreement, Arcturus common stock, and an option to purchase an additional 600,000 shares of Arcturus’

common stock at

Pursuant to the agreements, the Company paid $ 6.0 million in cash upfront to Arcturus and purchased 2,400,000 shares of Arcturus’ common stock at a stated value of $ 10.00 per share, resulting in a total of $ 30.0 million of consideration paid at the close of the transaction.

As a result, the Company received expanded license rights under the License Agreement, Arcturus common stock, and an option to purchase an additional 600,000 shares of Arcturus’ common stock at $ 16.00 per share.

In May 2020, the Company exercised its option to purchase 600,000 shares of Arcturus common stock for a total purchase price of $ 9.6 million.

The Company’s investment in Arcturus was accounted at fair value, as the fair value was readily determinable.

During the year ended December 31, 2022, the Company sold 500,000 shares of Arcturus common stock, at a weighted-average price of $ 20.39 per share.

As of December 31, 2022, the Company held no shares of Arcturus common stock.

ULTRAGENYX PHARMACEUTICAL INC.

Notes to Consolidated Financial Statements (continued)

$ 16.00 per share.

In May 2020, the Company exercised its option to purchase 600,000 shares of Arcturus common stock for a total purchase price of $ 9.6 million.

During the years ended December 31, 2022 and 2021 , the Company sold 500,000 shares and 1,700,000 shares of Arcturus common stock, at a weighted-average price of $ 20.39 and $ 47.44 , respectively.

As of December 31, 2022 and 2021 , the Company held nil and 500,000 shares, respectively, of Arcturus common stock.

The Company’s investment in Arcturus was accounted at fair value, as the fair value was readily determinable.

All remaining shares of Arcturus held by the Company were sold during the year ended December 31, 2022.

The changes in the fair value of the Company’s equity investment in Arcturus were as follows (in thousands):

Arcturus Common Stock

3 unchanged sentences

December 31, 2022

Change in fair value

Sale of shares

December 31, 2022

Daiichi Sankyo

1 unchanged sentence

Pursuant to the License Agreement, the Company granted Daiichi Sankyo a non-exclusive license to intellectual property, including know-how and patent applications, with respect to its Pinnacle PCL TM producer cell line platform, or Pinnacle PCL Platform, and HEK293 transient transfection manufacturing technology platforms for AAV-based gene therapy products.

The Company retains the exclusive right to use the manufacturing technology for its current target indications and additional indications identified now and in the future.

The Company will provide certain technical assistance and technology transfer services during the technology transfer period of three years to enable Daiichi Sankyo to use the technologies for its internal gene therapy programs.

Daiichi Sankyo has an option to extend the technology transfer period including know-how improvements by two additional one-year periods by paying a fixed amount for each additional year.

Daiichi Sankyo will be responsible for the manufacturing, development, and commercialization of products manufactured with the licensed technology;

however, the Company has the option to co-develop and co-commercialize rare disease products at the IND stage.

The Company may also provide strategic consultation to Daiichi Sankyo on the development of both AAV-based gene therapy products and other products for rare diseases.

Under the terms of the License Agreement, Daiichi Sankyo made an upfront payment of $ 125.0 million and an additional $ 25.0 million payment upon completion of the technology transfer of the Pinnacle PCL Platform and HEK293 platform.

Daiichi Sankyo reimbursed the Company for all costs associated with the transfer of the manufacturing technology and will pay single-digit royalties on net sales of products manufactured in either system.

The Company also entered into a Stock Purchase Agreement, or SPA, with Daiichi Sankyo, pursuant to which Daiichi Sankyo purchased 1,243,913 shares of the Company’s common stock in exchange for $ 75.0 million in cash during the first quarter of 2020.

Under the terms of the License Agreement, Daiichi Sankyo made an upfront payment of $ 125.0 million and an additional $ 25.0 million upon completion of the technology transfer of the Pinnacle PCL Platform and HEK293 platform.

Daiichi Sankyo reimbursed the Company for all costs associated with the transfer of the manufacturing technology.

The fair market value of the common stock issued to Daiichi Sankyo was $ 55.3 million based on the stock price of $ 44.43 per share on the date of issuance, resulting in a $ 19.7 million premium on the SPA.

Daiichi Sankyo is also subject to a three-year standstill and restrictions on sale of the shares (subject to customary exceptions or release).

In June 2020, the Company executed a subsequent license agreement, or the Sublicense Agreement, with Daiichi Sankyo for transfer of certain technology in consideration for an upfront payment of $ 8.0 million and annual maintenance fees, milestone payments, and royalties on any net sales of products incorporating the licensed intellectual property.

The License Agreement, the Sublicense Agreement, and the SPA are being accounted for as one arrangement because they were entered into at or near the same time and negotiated in contemplation of one another.

The Company evaluated the License Agreement and the Sublicense Agreement under ASC 606 and determined that the performance obligations under the agreements are (i) intellectual property with respect to its Pinnacle PCL Platform and HEK293 transient transfection manufacturing technology platform together with the initial technical assistance and technology transfer services, which was completed in the first quarter of 2022, and (ii) the transfer of any know-how and improvements after the completion of the initial technology transfer through the end of the three year technology transfer period ending March 2023.

ULTRAGENYX PHARMACEUTICAL INC.

Notes to Consolidated Financial Statements (continued)

As of December 31, 2022, the Company has determined that the total transaction price of the License Agreement was $ 183.3 million which was comprised of the $ 19.7 million premium from the SPA, the $ 125.0 million upfront payment, the $ 25.0 million in unconstrained milestone payments, $ 8.0 million from the Sublicense Agreement, and the $ 5.6 million estimated reimbursement amount for delivering the license and technology services.

Total revenue recognized under the license agreement through December 31, 2022 was $ 181.9 million.

The Company evaluated the License Agreement and the Sublicense Agreement under ASC 606 and determined that the performance obligations under the agreements are (i) intellectual property with respect to its Pinnacle PCL Platform and HEK293 transient transfection manufacturing technology platform together with the initial technical assistance and technology transfer services, and (ii) the transfer of any know-how and improvements after the completion of the initial technology transfer through the end of the three year technology transfer period.

The Company allocated the total transaction price to the two performance obligations on a relative stand-alone selling price basis.

Revenue allocated to the intellectual property and the technology transfer services was recognized over an initial period which was completed during the first quarter of 2022.Progress toward complete satisfaction of the individual performance obligation used an input measure.

Revenue for know-how and improvements after the completion of technology transfer is recognized on a straight-line basis over the remaining technology transfer period, which ends in March 2023, as it is expected that Daiichi Sankyo will receive and consume the benefits consistently throughout the period.

Royalties from commercial sales will be accounted for as revenue upon achievement of such sales, assuming all other revenue recognition criteria are met.

The Company recognized $ 7.7 million, $ 85.0 million, and $ 89.2 million respectively, for the years ended December 31, 2022, 2021, and 2020 in revenue related to this arrangement.

As of December 31, 2022 and 2021 , the Company had recorded contract liabilities of $ 1.5 million and $ 9.1 million and an accounts receivable related to the above agreements of nil and $ 0.1 million, respectively.

In December 2020, the Company entered into a License and Collaboration Agreement with Mereo BioPharma 3, or Mereo, to collaborate on the development of setrusumab.

Revenue allocated to the intellectual property and the technology transfer services was recognized over an initial period which was completed during the first quarter of 2022, measuring the progress toward complete satisfaction of the individual performance obligation using an input measure.

Revenue for know-how and improvements after the completion of technology transfer was recognized on a straight-line basis over the remaining technology transfer period, which ended in March 2023, as it was expected that Daiichi Sankyo would receive and consume the benefits consistently throughout the period.

The Company’s current obligations under the License Agreement and the Sublicense Agreement were completed following the conclusion of the technology transfer period.

Total revenue recognized under the arrangement through December 31, 2023 was $ 183.3 million.

The Company recognized $ 1.5 million, $ 7.7 million, and $ 85.0 million for the years ended December 31, 2023, 2022, and 2021 , respectively, in revenue related to this arrangement.

Accordingly, the Company recorded contract liabilities of nil and $ 1.5 million, net, for this arrangement as of December 31, 2023 and 2022, respectively.

In December 2020, the Company entered into a License and Collaboration Agreement with Mereo to collaborate on the development of setrusumab.

Under the terms of the agreement, the Company will lead future global development of setrusumab in both pediatric and adult patients with OI.

The Company was granted an exclusive license to develop and commercialize setrusumab in the U.S., Turkey, and the rest of the world, excluding the EEA, U.K., and Switzerland, or the Mereo territory, where Mereo retains commercial rights.

The Company was granted an exclusive license to develop and commercialize setrusumab in the U.S., Turkey, and the rest of the world, excluding the European Economic Area, United Kingdom, and Switzerland, or the

ULTRAGENYX PHARMACEUTICAL INC.

Notes to Consolidated Financial Statements (continued)

Mereo Territory, where Mereo retains commercial rights.

Each party will be responsible for post-marketing commitments and commercial supply in their respective territories.

2 unchanged sentences

Although Mereo is a variable interest entity, the Company is not the primary beneficiary as it does not have the power to direct the activities that would most significantly impact the economic performance of Mereo.

Prior to the achievement of certain development milestones, all consideration paid to Mereo represents rights to potential future benefits associated with Mereo’s in-process research and development activities, which have not reached technological feasibility and have no alternative future use.

Accordingly, for the three months ended March 31, 2021, the Company recorded the upfront payment of $ 50.0 million as in-process research and development expense.

For the years ended December 31, 2023, 2022, and 2021 , the Company recorded research and development expense of $ 9.0 million for the achievement of a clinical milestone, nil , and $ 50.0 million for the upfront payment, respectively.

In January 2022, the Company announced a collaboration with Regeneron Pharmaceuticals, or Regeneron, to commercialize Evkeeza for HoFH outside of the U.S.

3 unchanged sentences

The Company is obligated to pay up to $ 63.0 million in future milestone payments, contingent upon the achievement of certain regulatory and sales milestones.

The Company may share in certain costs for global trials led by Regeneron and also received the right to opt into other potential indications, including a right to negotiate a separate agreement with Regeneron to collaborate on the Regeneron’s investigational antibody for the treatment of fibrodysplasia ossificans progressiva, or FOP, which expired in July 2022.

The Company may share in certain costs for global trials led by Regeneron and also received the right to opt into other potential indications.

The collaboration agreement is within the scope of ASC 808 which provides guidance on the presentation and disclosure of collaborative arrangements.

As the Company would be the principal in future sale transactions with the customer, the Company will recognize product sales and cost of sales in the period the related sales occur and the related revenue recognition criteria are met.

ULTRAGENYX PHARMACEUTICAL INC.

Notes to Consolidated Financial Statements (continued)

Under the collaboration agreement, Regeneron will supply the product and will charge the Company a transfer price from the low 20 % range up to 40 % on net sales, which will be recognized as cost of sales in the Company’s Statement of Operations.

Upon the closing of the transaction in January 2022, the Company paid Regeneron a $ 30.0 million upfront payment.

The Company recorded costs of sales of $ 2.9 million, for the year ended December 31, 2022 , related to the amortization of the intangible asset.

Further, the Company reimbursed Regeneron for certain costs of $ 7.3 million that was recorded as research and development expense for the year ended December 31, 2022 .

No sales of Evkeeza were recorded for the year ended December 31, 2022.

Under the collaboration agreement, Regeneron supplies the product and charges the Company a transfer price from the low 20 % range up to 40 % on net sales, which is recognized as cost of sales in the Company’s Statement of Operations.

The Company paid Regeneron a $ 30.0 million upfront payment upon the closing of the transaction in January 2022, and d uring the year ended December 31, 2023, a $ 10.0 million regulatory milestone was achieved.

As these payments are for the Company’s use of intellectual property for Evkeeza for HoFH, they were recorded as intangible assets.

See Note 5 for additional details.

Under the collaboration agreement, the Company reimbursed Regeneron for development costs of $ 7.6 million, $ 7.3 million, and nil for the years ended December 31, 2023, 2022, and 2021, respectively, which were recorded as research and development expense on the Consolidated Statements of Operations.

The Company had collaboration payables for this arrangement included in accrued liabilities on the Consolidated Balance Sheets of $ 10.6 million and $ 6.8 million as of December 31, 2023 and December 31, 2022, respectively.

A dditionally, Regeneron is owed a transfer price fee and royalties on certain revenues and the Company recorded amounts owed to Regeneron of $ 0.7 million in cost of sales on the Consolidated Statements of Operations for the year ended December 31, 2023.

In May 2022, the Company announced an exclusive License Agreement for the AAV gene therapy for UX111 with Abeona for the treatment of MPS IIIA.

Under the terms of the agreement, the Company assumed responsibility for the UX111 program and in return, Abeona is eligible to receive tiered royalties of up to 10 % on net sales and commercial milestone payments of up to $ 30.0 million following regulatory approval of the product.

Additionally, the Company entered into an Assignment and Assumption Agreement with Abeona to transfer and assign to the Company the exclusive license agreement between Nationwide Children’s Hospital, or NCH, and Abeona for certain rights related to UX111.

Under this agreement, NCH is eligible to receive from the Company up to $ 1.0 million in development and regulatory milestones as well as royalties in the low single-digits of net sales.

ULTRAGENYX PHARMACEUTICAL INC.

Notes to Consolidated Financial Statements (continued)

The Company is obligated to pay Abeona certain prior development costs and other transition costs related to UX111.

Prior to product regulatory approval, all consideration paid to Abeona represents rights to potential future benefits associated with Abeona’s in-process research and development activities, which have not reached technological feasibility and have no alternative future use.

Accordingly, the value of the acquired intellectual property rights and clinical inventory as well as prior development costs and transition costs of $ 3.1 million, were recorded as research and development expense for the year ended December 31, 2022.

The Company did no t incur any other material costs related to this agreement in the years presented.

Solid Biosciences, Inc.

In October 2020, the Company entered into a strategic Collaboration and License Agreement with Solid Biosciences Inc., or Solid, and received an exclusive license for any pharmaceutical product that expresses Solid’s proprietary microdystrophin construct from AAV8 and variants thereof in clade E for use in the treatment of Duchenne muscular dystrophy and other diseases resulting from lack of functional dystrophin, including Becker muscular dystrophy.

The Company is collaborating to develop products that combine Solid’s differentiated microdystrophin construct, the Company’s Pinnacle PCL Platform, and the Company’s AAV8 variants.

Solid is providing development support and was granted an exclusive option to co-invest in products the Company develops for profit-share participation in certain territories.

1 unchanged sentence

The royalty rate changes to mid- to high double-digit percentage if Solid decides to co-invest in the product.

The Company also entered into a Stock Purchase Agreement and the Investor Agreement with Solid, pursuant to which, the Company purchased 7,825,797 shares of Solid’s common stock for an aggregate purchase price of $ 40.0 million.

In October 2022, Solid announced a 1 for 15 reverse stock split.

After the split, the Company holds 521,719 shares in Solid.

The Company’s investment in Solid is being accounted at fair value, as the fair value is readily determinable.

After the split, the Company held 521,719 shares of Solid's common stock.

The Company’s investment in Solid is being accounted at fair value, as the fair value is readily determinable.

The Company recorded the common stock investment at $ 26.8 million on the transaction date, which was based on the quoted market price on the closing date.

Although Solid is a variable interest entity, the Company is not the primary beneficiary as it does not have the power to direct the activities that would most significantly impact the economic performance of Solid.

Prior to the achievement of certain development milestones, all consideration paid to Solid represents rights to potential future benefits associated with Solid’s in-process research and development activities, which have not reached technological feasibility and have no alternative future use.

Accordingly, the remaining $ 13.2 million of the total $ 40.0 million paid as consideration was attributed to the license rights obtained and was recorded as in-process research and development expense during the year ended December 31, 2020.

ULTRAGENYX PHARMACEUTICAL INC.

Notes to Consolidated Financial Statements (continued)

The changes in the fair value of the Company’s investment in Solid’s common stock were as follows (in thousands):

Solid Common Stock

4 unchanged sentences

December 31, 2023

The Company leases office space and research, testing and manufacturing laboratory space in various facilities in Novato and Brisbane, California, in Cambridge and Woburn, Massachusetts, and in certain foreign countries, under operating agreements expiring at various dates through 2028 .

Certain lease agreements include options for the Company to extend the lease for multiple renewal periods and also provide for annual minimum increases in rent, usually based on a consumer price index or annual minimum increases.

The Company leases office space and research, testing and manufacturing laboratory space in various facilities in Novato and Brisbane, California, in Somerville, and Woburn, Massachusetts, and in certain foreign countries, under operating agreements expiring at various dates through 2029 .

Certain lease agreements include options for the Company to extend the lease for multiple renewal periods and provide for annual minimum increases in rent, usually based on a consumer price index or annual minimum increases.

None of these optional periods have been considered in the determination of the right-of-use lease asset or the lease liability for the leases as the Company did not consider it reasonably certain that it would exercise any such options.

1 unchanged sentence

The variable lease expense primarily consists of common area maintenance and other operating costs.

ULTRAGENYX PHARMACEUTICAL INC.

Notes to Consolidated Financial Statements (continued)

The components of lease expense were as follows (in thousands):

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Cash paid for amounts included in the measurement of operating lease liabilities for the years ended December 31, 2023, 2022, and 2021 was $ 13.4 million, $ 13.1 million, and $ 11.8 million, respectively, and was included in net cash used in operating activities in the Consolidated Statements of Cash Flows.

Right-of-use lease assets were $ 23.9 million and $ 26.0 million as of December 31, 2023 and 2022, respectively, and were included in other non-current assets on the Consolidated Balance Sheets.

The following table summarizes maturities of lease liabilities and the reconciliation of lease liabilities as of December 31, 2023:

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Lease liabilities , non-curre nt

The table above excludes $ 23.4 million of legally binding minimum lease payments for a lease that was executed during the year ended December 31, 2022, but whose term had not commenced.

The Company is also obligated to pay $ 9.9 million of fit-out costs related to this lease.

Lease liabilities are based on the net present value of the remaining lease payments over the remaining lease term.

For the years ended December 31, 2022 and 2021 , the weighted-average remaining operating lease terms were 3.01 years and 3.84 years, respectively, the weighted-average remaining financing lease terms were 2.81 years and 3.88 years, respectively, the weighted-average discount rates used to determine the lease liability for operating leases were 6.72 % and 6.64 %, respectively, and the weighted-average discount rates used to determine the lease liability for finance leases were 5.13 % and 5.44 % respectively.

ULTRAGENYX PHARMACEUTICAL INC.

Notes to Consolidated Financial Statements (continued)

For the years ended December 31, 2023 and 2022 , the weighted-average remaining operating lease terms were 4.5 years and 3.0 years, the weighted-average remaining financing lease terms were nil and 2.8 years, the weighted-average discount rates used to determine the lease liability for operating leases were 9.6 % and 6.7 %, and the weighted-average discount rates used to determine the lease liability for finance leases were nil and 5.1 % respectively.

Liabilities for Sales of Future Royalties

In December 2019, the Company entered into a Royalty Purchase Agreement with RPI.

Pursuant to the agreement, RPI paid $ 320.0 million to the Company in consideration for the right to receive royalty payments effective January 1, 2020, arising from the net sales of Crysvita in the EU, the U.K., and Switzerland under the terms of the Company’s Collaboration and License Agreement with KKC dated August 29, 2013, as amended, or the KKC Collaboration Agreement.

The agreement with RPI will automatically terminate, and the payment of royalties to RPI will cease, in the event aggregate royalty payments received by RPI are equal to or greater than $ 608.0 million prior to December 31, 2030, or in the event aggregate royalty payments received by RPI are less than $ 608.0 million prior to December 31, 2030, or when aggregate royalty payments received by RPI are equal to $ 800.0 million.

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and Canada under the terms of the KKC Collaboration Agreement.

The calculation of royalty payments to OMERS will be based on net sales of Crysvita beginning in April 2023 and will expire upon the earlier of the date on which aggregate payments received by OMERS equals $ 725.0 million or the date the final royalty payment is made to the Company under the KKC Collaboration Agreement.

The calculation of royalty payments to OMERS is based on net sales of Crysvita beginning in April 2023 and will expire upon the earlier of the date on which aggregate payments received by OMERS equals $ 725.0 million or the date the final royalty payment is made to the Company under the KKC Collaboration Agreement.

Proceeds from these transactions were recorded as liabilities for sales of future royalties on the Consolidated Balance Sheets.

Upon inception of the respective arrangements, the Company recorded $ 320.0 million and $ 500.0 million, net of transaction costs of $ 5.8 million and $ 9.1 million for RPI and OMERS, respectively, using the effective interest method over the estimated life of the applicable arrangement.

In order to determine the amortization of the liabilities, the Company is required to estimate the total amount of future royalty payments to be received by the Company and paid to RPI and OMERS, subject to the capped amount, over the life of the arrangements.

The excess of future estimated royalty payments (subject to the capped amount), over the $ 314.2 million and $ 491.0 million, respectively, of net proceeds, is recorded as non-cash interest expense over the life of the arrangements.

In order to determine the amortization of the liabilities, the Company is required to estimate the total

ULTRAGENYX PHARMACEUTICAL INC.

Notes to Consolidated Financial Statements (continued)

amount of future royalty payments to be received by the Company and paid to RPI and OMERS, subject to the capped amount, over the life of the arrangements.

The excess of future estimated royalty payments (subject to the capped amount) to RPI and OMERS, over the $ 314.2 million and $ 491.0 million, respectively, of net proceeds, is recorded as non-cash interest expense over the life of the arrangements.

Consequently, the Company estimates an imputed interest on the unamortized portion of the liabilities and records interest expense relating to the transactions.

The Company records the royalty revenue arising from the net sales of Crysvita in the applicable territories as non-cash royalty revenue in the Consolidated Statements of Operations over the term of the arrangements.

The Company records the royalty revenue arising from the net sales of Crysvita in the applicable territories as royalty revenue in the Consolidated Statements of Operations over the term of the arrangements.

Royalties earned under the RPI and OMERS arrangements from inception to December 31, 2023 have been $ 73.4 million and $4 8.6 million, respectively.

The Company periodically assesses the expected royalty payments using a combination of historical results, internal projections and forecasts from external sources.

To the extent such payments are greater or less than the Company’s initial estimates or the timing of such payments is materially different than its original estimates, the Company will prospectively adjust the amortization of the liabilities and the effective interest rate.

The Company’s effective annual interest rate was approximately 9.3 % and 8.4 %, for RPI and OMERS, respectively, as of December 31, 2022.

There are a number of factors that could materially affect the amount and timing of royalty payments from KKC in the applicable territories, most of which are not within the Company’s control.

Such factors include, but are not limited to, the success of KKC’s sales and promotion of Crysvita, changing standards of care, delays or disruptions related to the COVID-19 pandemic, macroeconomic and inflationary pressures, the introduction of competing products, pricing for reimbursement in various territories, manufacturing or other delays, intellectual property matters, adverse events that result in governmental health authority imposed restrictions on the use of Crysvita, significant changes in foreign exchange rates as the royalty payments are made in U.S.

dollars, or USD, while significant portions of the underlying sales of Crysvita are made in currencies other than USD, and other events or circumstances that could result in reduced royalty payments from sales of Crysvita, all of which would result in a reduction of non-cash royalty revenue and the non-cash interest expense over the life of the arrangement.

Conversely, if sales of Crysvita in the relevant territories are more than expected, the non-cash royalty revenue and the non-cash interest expense recorded by the Company would be greater over the term of the arrangements.

The Company’s effective annual interest rates were 6.2 % and 7.8 %, for RPI and OMERS, respectively, as of December 31, 2023.

There are a number of factors that could materially affect the amount and timing of royalty payments from KKC in the applicable territories, most of which are not within the Company’s control.

Such factors include, but are not limited to, the success of KKC’s sales and promotion of Crysvita, changing standards of care, macroeconomic and inflationary pressures, the introduction of competing products, pricing for reimbursement in various territories, manufacturing or other delays, intellectual property matters, adverse events that result in governmental health authority imposed restrictions on the use of Crysvita, significant changes in foreign exchange rates as the royalty payments are made in U.S.

dollars, or USD, while significant portions of the underlying sales of Crysvita are made in currencies other than USD, and other events or circumstances that could result in reduced royalty payments from sales of Crysvita, all of which would result in a reduction of royalty revenue and the non-cash interest expense over the life of the arrangement.

Conversely, if sales of Crysvita in the relevant territories are more than expected, the royalty revenue and the non-cash interest expense recorded by the Company would be greater over the term of the arrangements.

The following table shows the activity within the liability account (in thousands):

ULTRAGENYX PHARMACEUTICAL INC.

Notes to Consolidated Financial Statements (continued)

Liabilities for Sales of Future Royalties

December 31, 2021

Non-cash collaboration royalty revenue

Net proceeds from sale of future

Royalty revenue

Non-cash interest expense

December 31, 2022

Net proceeds from sale of future

Non-cash collaboration royalty revenue

Royalty revenue

Non-cash interest expense

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At-the-Market Offerings

In May 2021, the Company entered into an Open Market Sale Agreement with Jefferies LLC, or Jefferies, pursuant to which the Company may offer and sell shares of the Company’s common stock having an aggregate offering proceeds up to $ 350.0 million, from time to time, in ATM offerings through Jefferies.

As of December 31, 2022 , the Company has sold 1,050,372 shares under the arrangement resulting in net proceeds of approximately $ 78.9 million.

No shares were sold under the arrangement for the year ended December 31, 2022.

During the year ended December 31, 2023, there were 1,175,584 shares sold under the ATM resulting in net proceeds of $ 53.3 million.

There were no shares sold under the ATM for year ended December 31, 2022.

As of December 31, 2023 , the Company has sold a total of 2,225,956 shares under the ATM, resulting in net proceeds of $ 132.2 million.

Underwritten Public Offering

In October 2020, the Company completed an underwritten public offering in which 5,111,110 shares of common stock were sold, which included 666,666 shares purchased by the underwriters pursuant to an option granted to them in connection with the offering, at a public offering price of $ 90.00 per share.

The total proceeds that the Company received from the offering were approximately $ 435.6 million, net of underwriting discounts and commissions.

In October 2023, the Company completed an underwritten public offering in which 9,833,334 shares of common stock were sold, including the exercise in full by the underwriters of their option to purchase an additional 1,500,000 shares, at a public offering price of $ 30.00 per share.

In connection with the offering, the Company sold to certain investors pre-funded warrants, in lieu of common stock, to purchase 1,666,722 shares of common stock at a purchase price of $ 29.999 per pre-funded warrant, which equals the public offering price per share of common stock less the $ 0.001 exercise price per share of each pre-funded warrant.

ULTRAGENYX PHARMACEUTICAL INC.

Notes to Consolidated Financial Statements (continued)

proceeds that the Company received from the offering were $ 326.5 million, net of underwriting discounts and commissions.

As of December 31, 2023 , no ne of the pre-funded warrants had been exercised.

The pre-funded warrants were classified as a component of permanent equity in the Company's Consolidated Balance Sheets as they are freestanding financial instruments that are immediately exercisable, do not embody an obligation for the Company to repurchase its own shares and permit the holders to receive a fixed number of shares of common stock upon exercise.

All of the shares underlying the pre-funded warrants have been included in the weighted-average number of shares of common stock used to calculate net loss per share, basic and diluted, attributable to common stockholders because the shares may be issued for little or no consideration, are fully vested, and are exercisable after the original issuance date of the pre-funded warrants.

Stock-Based Awards

Equity Plan Awards

In 2011, the Company adopted the 2011 Equity Incentive Plan, or the 2011 Plan.

The 2011 Plan provides for the granting of stock-based awards to employees, directors, and consultants under terms and provisions established by the board of directors.

In 2014, the Company adopted the 2014 Incentive Plan, or the 2014 Plan.

The 2014 Plan had 2,250,000 shares of common stock available for future issuance at the time of its inception, which included 655,038 shares available under the 2011 Plan, which were transferred to the 2014 Plan upon adoption.

No further grants subsequent to the IPO were made under the 2011 Plan.

The 2014 Plan provides for automatic annual increases in shares available for grant, beginning on January 1, 2015 through January 1, 2024 .

In February 2021, the Company adopted the Employment Inducement Plan, or the Inducement Plan, with a maximum of 500,000 shares available for grant under the Inducement Plan.

In 2014, the Company adopted the 2014 Incentive Plan, or the 2014 Plan, for the granting of stock-based awards to employees, directors, and consultants under terms and provisions established by the board of directors.

The 2014 Plan had 2,250,000 shares of common stock available for future issuance at the time of its inception.

The 2014 Plan provided for automatic annual increases in shares available for grant, beginning on January 1, 2015 through June 7, 2023 .

In June 2023, the Company adopted the 2023 Incentive Plan which had 4,500,000 shares of common stock available for future issuance at the time of its inception, plus the number of shares subject to the 2014 Plan cancelled after June 7, 2023.

No further shares were granted under the 2014 Plan after June 7, 2023.In February 2021, the Company adopted the Employment Inducement Plan, or the Inducement Plan, which was subsequently amended in June 2023 to provide for a maximum of 850,000 shares available for grant under the plan.

Under the terms of the 2023 Plan and Inducement Plan, awards may be granted at an exercise price not less than fair market value.

For employees holding more than 10 % of the voting rights of all classes of stock, the exercise prices for awards must be at least 110 % of fair market of the common stock on the grant date, as determined by the board of directors.

The exercise price of an option may not be less than the fair market value.

The term of an award granted under the 2023 Plan and Inducement Plan may not exceed ten years .

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As of December 31, 2023 , an aggregate of 19,610,125 shares of common stock have been authorized for issuance under the 2014 Plan, the 2023 Plan, and the Inducement Plan.

ULTRAGENYX PHARMACEUTICAL INC.

Notes to Consolidated Financial Statements (continued)

Stock Option Activity

The following table summarizes activity under the Company’s stock option plans and related information:

Options Outstanding

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(In thousands)

Outstanding —

December 31, 2021

Outstanding — December 31, 2022

Options granted

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Options cancelled

Outstanding —

December 31, 2022

Vested and exercisable —

December 31, 2022

Vested and expected to vest —

December 31, 2022

The aggregate intrinsic values of options outstanding, vested and exercisable, and vested and expected to vest were calculated as the difference between the exercise price of the options and the fair value of the Company’s common stock.

Outstanding — December 31, 2023

Vested and exercisable — December 31, 2023

Vested and expected to vest — December 31, 2023

The total intrinsic value of options exercised during the years ended December 31, 2023, 2022, and 2021 was $ 4.9 million, $ 2.6 million, and $ 38.8 million, respectively.

Cash received from the exercise of options was $ 2.7 million, $ 6.2 million, and $ 36.6 million for the years ended December 31, 2023, 2022, and 2021, respectively.

The weighted-average estimated fair value of stock options granted was $ 34.77 , $ 70.84 , and $ 35.22 per share of the Company’s common stock during the years ended December 31, 2022, 2021, and 2020, respectively.

ULTRAGENYX PHARMACEUTICAL INC.

Notes to Consolidated Financial Statements (continued)

The weighted-average estimated fair value of stock options granted was $ 25.53 , $ 34.77 , and $ 70.84 per share of the Company’s common stock during the years ended December 31, 2023, 2022, and 2021, respectively.

The total estimated grant date fair value of options vested during the years ended December 31, 2023, 2022, and 2021 was $ 59.7 million, $ 58.7 million, and $ 48.1 million, respectively.

Performance Stock Options

The following table summarizes activity under the Company’s Performance Stock Option, or PSO, plans and related information:

PSOs Outstanding

3 unchanged sentences

Aggregate Intrinsic Value

Outstanding —

December 31, 2021

Outstanding — December 31, 2022

PSOs cancelled

Outstanding —

December 31, 2022

Vested and exercisable —

December 31, 2022

Vested and expected to vest —

December 31, 2022

Outstanding — December 31, 2023

Vested and exercisable — December 31, 2023

Vested and expected to vest — December 31, 2023

During the year ended December 31, 2022, PSOs were granted to certain nonexecutive employees.

PSOs are subject to vest only if specified operational milestones are achieved and the employees’

continued service with the Company.

PSOs are subject to vest only if specified operational milestones are achieved and the employees’ continued service with the Company.

The Company uses the Black-Scholes method to calculate the fair value at the grant date and is recognizing stock-based compensation expense for the PSOs that are expected to vest.

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As of December 31, 2023, certain operational milestones were deemed probable of achievement.

The aggregate intrinsic values of PSOs outstanding, vested and exercisable, and vested and expected to vest were calculated as the difference between the exercise price of the PSOs and the fair value of the Company’s common stock.

No PSOs vested or were exercised during the year ended December 31, 2022.

The total estimated grant date fair value of PSOs vested during the year ended December 31, 2023 , was $ 3.4 million.

No PSOs were granted or were exercised during the year ended December 31, 2023.

The weighted-average estimated fair value of PSOs granted was $ 28.76 during the year ended December 31, 2022.

ULTRAGENYX PHARMACEUTICAL INC.

Notes to Consolidated Financial Statements (continued)

Restricted Stock Units

The following table summarizes activity under the Company’s Restricted Stock Units, or RSU, plans and related information:

RSUs Outstanding

Weighted- Average Grant Date Fair Value

Unvested —

December 31, 2021

Unvested — December 31, 2022

RSUs cancelled

Unvested —

December 31, 2022

The fair value of the RSUs is determined on the grant date based on the fair value of the Company’s common stock.

Unvested — December 31, 2023

The fair value of the RSUs is determined on the grant date based on the fair value of the Company’s common stock.

The fair value of the RSUs is recognized as expense ratably over the vesting period of one to four years .

1 unchanged sentence

The aggregate intrinsic value of the shares of the RSUs vested during the years ended December 31, 2023, 2022, and 2021 was $ 33.0 million, $ 37.8 million, and $ 69.9 million, respectively.

ULTRAGENYX PHARMACEUTICAL INC.

Notes to Consolidated Financial Statements (continued)

Performance Stock Units

The following table summarizes activity under the Company’s Performance Stock Units, or PSUs, from the 2014 Plan and related information:

The following table summarizes activity under the Company’s Performance Stock Units, or PSUs and related information:

PSUs Outstanding

Weighted- Average Grant Date Fair Value

Unvested —

December 31, 2021

Unvested — December 31, 2022

PSUs cancelled

Unvested —

December 31, 2022

The fair value of the PSUs is determined on the grant date based on the fair value of the Company’s common stock, except for certain PSUs with a market vesting condition, for which fair value is estimated using a Monte Carlo simulation model.

PSUs are subject to vest only if certain specified criteria are achieved and the employees’

continued service with the Company after achievement of the specified criteria.

Unvested — December 31, 2023

PSUs are subject to vest only if certain specified criteria are achieved and the employees’ continued service with the Company.

For certain PSUs, the number of PSUs that may vest are also subject to the achievement of certain specified criteria, including both performance conditions and market conditions.

As of December 31, 2022, the specified criteria were deemed probable of achievement or already achieved.

As of December 31, 2023, certain specified criteria were deemed probable of achievement or already achieved.

Stock-based compensation for PSUs is recognized over the service period beginning in the period the Company determines it is probable that the performance criteria will be achieved.

1 unchanged sentence

Employee Stock Purchase Plan

In January 2014, the Company adopted the 2014 Employee Stock Purchase Plan, or ESPP, and reserved a total of 600,000 shares of common stock for issuance under the ESPP.

The ESPP provides for automatic annual increases in shares available for grant, beginning on January 1, 2015 through January 1, 2024 .

Eligible employees may purchase common stock at 85 % of the lesser of the fair market value of common stock on the offering date or the purchase date with a six-month look-back feature.

ESPP purchases are settled with common stock from the ESPP’s previously authorized and available pool of shares.

In January 2014, the Company adopted the 2014 Employee Stock Purchase Plan, or ESPP, which was amended and restated in June 2023.

Under the ESPP, eligible employees may purchase common stock at 85 % of the lesser of the fair market value of common stock on the offering date or the purchase date with a six-month look-back feature.

ESPP purchases are settled with common stock from the ESPP’s previously authorized and available pool of shares.

During the year ended December 31, 2023 , the Company issued 195,462 shares of common stock under the ESPP.

As of December 31, 2023 , an aggregate of 6,609,795 shares of common stock have been authorized for future issuance on the ESPP.

ULTRAGENYX PHARMACEUTICAL INC.

Notes to Consolidated Financial Statements (continued)

Stock-Based Compensation Expense

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Each of these inputs is subjective and generally requires significant judgment to determine.

Expected Term —The Company’s expected term represents the period that the Company’s stock-based awards are expected to be outstanding and is determined using the simplified method (based on the mid-point between the vesting date and the end of the contractual term).

Expected Volatility —The Company’s expected volatility is based on historical volatility over the look-back period corresponding to the expected term.

Risk-Free Interest Rate —The risk-free interest rate is based on the U.S.

Expected Volatility —The Company’s expected volatility is based on historical volatility over the look-back period corresponding to the expected term.

ULTRAGENYX PHARMACEUTICAL INC.

Notes to Consolidated Financial Statements (continued)

Risk-Free Interest Rate —The risk-free interest rate is based on the U.S.

Treasury zero coupon issues in effect at the time of grant for periods corresponding with the expected term of option.

Expected Dividend —The Company has never paid dividends on its common stock and has no plans to pay dividends on its common stock.

Therefore, the Company used an expected dividend yield of zero.

8 unchanged sentences

Year Ended December 31,

Expected term (years)

Expected term in years

Expected volatility

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The Company recorded $ 9.7 million, $ 9.0 million, and $ 5.5 million as expense related to the plan for the years ended December 31, 2023, 2022, and 2021 , respectively.

ULTRAGENYX PHARMACEUTICAL INC.

Notes to Consolidated Financial Statements (continued)

The components of the Company’s loss before income taxes were as follows (in thousands):

Year Ended December 31,

Total loss before income taxes

The components of the Company’s income tax provision were as follows (in thousands):

ULTRAGENYX PHARMACEUTICAL INC.

Notes to Consolidated Financial Statements (continued)

The components of the Company’s income tax provision were as follows (in thousands):

Year Ended December 31,

5 unchanged sentences

Total deferred tax provision

Total provision for income taxes

Total (benefit from) provision for income taxes

The Company has incurred net operating losses since inception.

4 unchanged sentences

Due to this required capitalization of research and development expenditures and the significant taxable income generated as a result of our sale of royalties in July 2022, the Company has recorded current state income tax expense of $ 6.1 million for the year ended December 31, 2022.

The current income tax provision is primarily for state taxes the Company anticipates paying as a result of statutory limitations on the Company's ability to offset expected taxable income with net operating loss carry forwards in certain states.

For the year ended December 31, 2023, the Company recognized an income tax benefit of $ 4.8 million attributable to modifications in its state apportionment methodology.

The Company realized no benefit for current year losses due to a full valuation allowance against the U.S.

net deferred tax assets.

The benefit was offset by an income tax expense of $ 3.0 million from foreign jurisdictions.

The effective tax rate of our provision for income taxes differs from the federal statutory rate as follows:

3 unchanged sentences

Federal tax credits

Premium on equity issuance

Nondeductible permanent items

29 unchanged sentences

As of December 31, 2023 and 2022 , the Company had federal Orphan Drug Credits of $ 269.6 million and $ 239.3 million, respectively, available to reduce future tax liabilities that will begin to expire in 2031 .

The Company’s ability to use net operating loss and tax credit carryforwards to reduce future taxable income and liabilities may be subject to annual limitations pursuant to Internal Revenue Code Sections 382 and 383 as a result of ownership changes in the past and future.

As a result of ownership changes in 2012 and 2011, $ 3.6 million of federal net operating loss carryforwards, $ 3.6 million of state net operating loss carryforwards, and $ 0.2 million of federal tax credits are permanently limited.

1 unchanged sentence

The valuation allowance increased by $ 141.3 million and $ 193.8 million during the years ended December 31, 2023 and 2022, respectively.

Due to a change in the state tax rates, the Company recorded a net decrease to the deferred tax liability of $ 1.6 million with a corresponding deferred income tax benefit of $ 1.6 million for the year ended December 31, 2023.

ULTRAGENYX PHARMACEUTICAL INC.

Notes to Consolidated Financial Statements (continued)

The Company recorded unrecognized tax benefits for uncertainties in income taxes.

A reconciliation of the Company’s unrecognized tax benefits follows (in thousands):

Balance at beginning of year

3 unchanged sentences

Balance at end of year

ULTRAGENYX PHARMACEUTICAL INC.

Notes to Consolidated Financial Statements (continued)

The entire amount of the unrecognized tax benefits would not impact the Company’s effective tax rate if recognized.

Approximately $ 1.3 million in unrecognized tax benefits would impact the Company’s effective tax rate if recognized.

The Company has elected to include interest and penalties as a component of tax expense.

During the years ended December 31, 2022, 2021, and 2020 , the Company did no t recognize accrued interest and penalties related to unrecognized tax benefits.

For the year ended December 31, 2023, the Company recognized accrued interest and penalties of $ 0.2 million as a component of income tax expense.

No accrued interest and penalties were recognized as a component of income tax expense during the years ended December 31, 2022 and 2021.

The Company does not anticipate that the amount of existing unrecognized tax benefits will significantly increase or decrease during the next year.

It is the Company’s intention to reinvest the earnings of its non-U.S.

subsidiaries in their operations.

2 unchanged sentences

The Company files income tax returns in the U.S.

federal, forty state tax jurisdictions, and ten foreign countries.

federal, 40 state tax jurisdictions, and ten foreign countries.

The federal and state income tax returns from inception to December 31, 2023 remain subject to examination.

7 unchanged sentences

Manufacturing and Services

The terms of certain of the Company’s licenses, royalties, development and collaboration agreements, as well as other research and development activities, require the Company to pay potential future milestone payments based on product development success.

The amount and timing of such obligations are unknown or uncertain.

These potential obligations are further described in “Note 8.

License and Research Agreements.”

See “Note 9.

Leases”

for lease commitments.

These potential obligations are further described in “Note 8.

License and Research Agreements.”

Leases” for lease commitments.

Contingencies

While there are no material legal proceedings the Company is aware of, the Company may become party to various claims and complaints arising in the ordinary course of business.

Management does not believe that any ultimate liability resulting from any of these claims will have a material adverse effect on its results of operations, financial position, or liquidity.

Management does not believe that any ultimate liability resulting from any of these potential claims will have a material adverse effect on its results of operations, financial position, or liquidity.

However, management cannot give any assurance regarding the ultimate outcome of these claims, and their resolution could be material to operating results for any particular period, depending upon the level of income for the period.

ULTRAGENYX PHARMACEUTICAL INC.

Notes to Consolidated Financial Statements (continued)

Guarantees and Indemnifications

The Company indemnifies each of its directors and officers for certain events or occurrences, subject to certain limits, while the director is or was serving at the Company’s request in such capacity, as permitted under Delaware law and in accordance with its certificate of incorporation and bylaws.

The term of the indemnification period lasts as long as a director may be subject to any proceeding arising out of acts or omissions of such director in such capacity.

The Company indemnifies each of its directors and officers for certain events or occurrences, subject to certain limits, while the director or officer is or was serving at the Company’s request in such capacity, as permitted under Delaware law and in accordance with its certificate of incorporation and bylaws.

The term of the indemnification period lasts as long as a director or officer may be subject to any proceeding arising out of acts or omissions of such director and officer in such capacity.

The maximum amount of potential future indemnification is unlimited;

however, the Company currently holds director liability insurance.

This insurance allows the transfer of risk associated with the Company’s exposure and may enable it to recover a portion of any future amounts paid.

The Company believes that the fair value of these indemnification obligations is minimal.

Accordingly, it has not recognized any liabilities relating to these obligations for any period presented.

ULTRAGENYX PHARMACEUTICAL INC.

Notes to Consolidated Financial Statements (continued)

Related Party Transaction

In July 2022, the Company entered into an agreement with a non-profit foundation in which two of the Company’s board members, including the Company’s Chief Executive Officer, are also board members of the foundation, whereby a $ 1.0 million contribution will be paid out to the foundation over a four-year period, beginning in the third quarter of 2022, to support rare disease education and awareness.

As a result, the Company recorded $ 0.3 million as research and development expense for this agreement for the year ended December 31, 2022 .

In July 2022, the Company entered into an agreement with a non-profit foundation in which two members of the Company’s board of directors, including the Company’s Chief Executive Officer, also serve as board members of the foundation, whereby an aggregate $ 1.0 million contribution is being paid to the foundation over a four-year period, beginning in the third quarter of 2022, to support rare disease education and awareness.

As a result, the Company recorded $ 0.3 million and $ 0.3 million as research and development expense for this agreement for the years ended December 31, 2023 and 2022 , respectively.

Net Loss per Share

6 unchanged sentences

Year Ended December 31,

Options to purchase common stock, RSUs, and PSUs

Options to purchase common stock,

restricted stock units, and performance stock units

Employee stock purchase plan

Common stock warrants

Accumulated Other Comprehensive Loss

Total accumulated other comprehensive loss consisted of the following (in thousands):

Accumulated Other Comprehensive Income (Loss)

Total accumulated other comprehensive income (loss) consisted of the following (in thousands):

Year Ended December 31,

Cumulative foreign currency translation adjustment

Unrealized loss on securities available-for-sale

Total accumulated other comprehensive loss

Unrealized gain (loss) on securities available-for-sale

Total accumulated other comprehensive income (loss)

Compared sentence by sentence after normalising whitespace, quotation marks, case and digits, so re-formatting and restated figures do not read as changed language. Wording changes appear as one removal and one addition. The current filing and the prior one are authoritative.

What changed 10-K

Item 9A. Controls and Procedures